PATENT ABSTRACT
This present disclosure generally relates to compositions and methods for cancer diagnosis, research and therapy, including but not limited to, cancer markers. In particular, the present disclosure provides a computerized method for detecting fusion transcripts from RNA-seq data and provides the fusion transcripts identified thereby in human cancers. Compositions and methods for identifying the fusion transcripts are also provided.

PATENT DESCRIPTION
CROSS-REFERENCE TO RELATED APPLICATIONS 
       [0001]    The present application is a continuation-in-part of U.S. patent application Ser. No. 13/372,180, filed Feb. 13, 2012, the contents of which are hereby incorporated by reference in its entirety. 
     
    
     REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY 
       [0002]    The content of the electronically submitted sequence listing, file name Human_Cancer_Fusion_Transcripts20150705.txt, size 176,469,241 bytes; and date of creation Jul. 5, 2015, filed herewith, is incorporated herein by reference in its entirety. 
       BACKGROUND OF THE INVENTION 
       [0003]    Cancer is one of the leading causes of deaths in the world and a class of heterogeneous complex diseases with multiple genes in diverse pathways involved in its initiation, uncontrolled growth, invasion, and metastasis. One of the cancer hallmarks is genetic instabilities that can result in chromosomal translocation, insertion, duplication, deletion, and inversion. These genetic alternations often cause fusion genes, which in turn are transcribed into fusion mRNAs or fusion transcripts (Mitelman, et al. 2007). Numerous methods have been developed to characterize the cancer genomic aberrations. Introduction of molecular cytogenetic technologies such as chromosomal fluorescence in situ hybridization (FISH) and multicolor FISH into the repertoire of clinical testing and genetic investigation has led to an explosion of information about chromosomal aberrations in cancers, which has greatly improved our understanding of the prevalence and variety of these genomic rearrangements. Comparative genomic hybridization (CGH) and—array CGH are developed to detect chromosomal aberration and copy-number variations in cancers. Applications of these technologies in clinical and genetic investigations have accumulated an abundance of information about chromosomal aberrations, which is stored in NCI&#39;s Cancer Chromosomes database (Mitelman, et al. 2015). 
         [0004]    Next-generation sequencing of transcriptomes (RNA-seq) is one of the most recent technological advances and provides one of the most important tools to unbiasedly profile gene expression and to uncover the novel splice sites. However, RNA-Seq faces several bioinformatics challenges from developing efficient methods to storing, retrieving and processing large amounts of RNA-Seq data, which disproportionally accumulate highly expressed mRNA sequences. Existence of spliceosomal introns in gene sequences, especially in the mammalian genes makes analyses of these short sequences more problematic and computationally expensive. To overcome these challenges, a number of softwares have been developed to profile gene expression and to identify novel alternatively-spliced splice sites and fusion transcripts. The software to be able to detect fusion transcripts include TopHat-Fusion, SOAPfusion, SnowShoes-FTD, ShortFuse, BreakFusion, ChimeraScan, Comrad, FusionAnalyser, deFuse, FusionMap, FusionHunter, FusionSeq, R-SAP, Trans-ABySS and Trinity. 
         [0005]    These technological advances have led to the identification of multiple novel fusion transcripts (Klijn, et al. 2015, Robinson, et al. 2011, Sakarya, et al. 2012). More recently, transcriptome sequencing and RNA-seq have been used to identify the fusion genes (Maher, et al. 2009, Zhao, et al. 2009). Using paired-end RNA sequencing, Maher et al. has identified 12 novel chimeric transcripts of fusion genes in 4 cancer cell line (Maher, et al. 2009). Edgren et al. have applied paired-end RNA-seq to identify 24 novel and 3 previously known fusion genes in breast cancer cells (Edgren, et al. 2011). The software improvement has led to the identification of more fusion transcripts (Kim and Salzberg 2011). Recently, Sakarya et al. have used next-generation sequencing to analyze MCF-7 breast cancers and have identified 40 novel fusion genes (Sakarya, et al. 2012). More recently, Klijn et al have performed comprehensive RNA-seq analysis of 675 human cancer cell lines and have identified 2,200 unique pairs of fusion genes, 1,435 of which had been previously not found (Klijn, et al. 2015). Many of these chimeric transcripts have shown to have multiple isoforms (Robinson, et al. 2011). The read-though fusion transcripts have been shown to be associated with breast cancer (Varley, et al. 2014). 
         [0006]    However, current approaches are inefficient to analyze large RNA-seq datasets. Majority of them often are very slow and require large memories and powerful computation systems. They are effective to uncover highly-expressed fusion transcripts and may be unable to discover lowly-expressed fusion transcripts. Because some algorithms used may be unintentional to remove some fusion transcripts from considerations. A large amounts of RNA-seq datasets have been accumulated in ENCODE (ENCODE 2015), ENA (ENA 2014) and NCBI (NCBI 2014). However, the numbers of fusion transcripts identified so far remain small considering cancer extreme heterogeneities and complexities. 
       SUMMARY OF THE INVENTION 
       [0007]    This application generally relates to a method for identifying fusion transcripts in cancers, and more specifically to a computerized method for identifying fusion transcripts from RNA sequencing data obtained from cancer cells. The application also relates to sequences of fusion transcripts identified by the above method. 
         [0008]    Previously, the applicant had disclosed a method of identifying exons and introns from predetermined genome data including nucleotide sequence data, predetermined 5′ and 3′ splicing junction data, and exon and intron data (U.S. Pat. No. 8,185,323). The contents of the above patent are hereby incorporated by reference in its entirety. 
         [0009]    The applicant had observed that recently-gained human spliceosomal introns had identical 5′ and 3′ splice sites (Zhuo, et al. 2007). Based on this finding, the applicant had found that both 5′ exonic sequences (E5) immediately upstream of introns and 3′ intronic sequences (13) were dynamically conserved and appears rather reminiscent of self-splicing group II ribozymes and of constraints imposed by base pairing between intronic-binding sites (IBSs) and exonic-binding sites (EBSs) (Zhuo, et al. 2012). Therefore, the applicant has proposed that both E5 and I3 sequences constitute splicing codes, which are deciphered by splicer proteins/RNAs via specific base-pairing (Zhuo, et al. 2012). This splicing code model suggested that a yet-to-be characterized splicer proteins/RNA would decode identical sequences in all pre-mRNAs in conjugation with U snRNAs and spliceosomes, regardless whether the E5 and I3 sequences are in the one molecule or two different molecules. 
         [0010]    Based on this splicing code model, the applicant has developed a simple, accurate and fast computation system to analyze RNA-seq data for the discovery of fusion transcripts, and has identified a large number of novel fusion transcripts, some of which can be used for early detection and prognosis of cancer. 
         [0011]    Disclosed herein includes a method of detecting alternatively spliced transcripts or fusion transcripts in at least one RNA sequence obtained from biochemical analysis of a biological sample from a species or from a database, comprising the steps of: 
         [0012]    (a) providing a computer for data identification, aligning, and comparison purposes, wherein the computer has access to predetermined genome data of said species, comprising data of predetermined genomic nucleotide sequences, predetermined splicing junctions, predetermined exons, predetermined introns, and annotated genes; 
         [0013]    (b) generating a splicing code table using the predetermined genome data, the splicing code table comprising ordered E5 keys, I5 keys, E3 keys and I3 keys, wherein the E5 keys, the I5 keys, the E3 keys and the I3 keys are subsequences of predetermined 5′ exonic (E5), 5′ intronic (I5), 3′ exonic (E3), and 3′ intronic (I3) splicing sequences for each of the predetermined splicing junctions respectively; 
         [0014]    (c) aligning the at least one RNA sequence with each of the E5 keys and each of the E3 keys in the splicing code table; and 
         [0015]    (d) determining that the at least one RNA sequence is an alternatively spliced transcript if: the at least one RNA sequence contains a first subsequence substantially identical to an E5 key of a first splicing junction and a second subsequence substantially identical to an E3 key of a second splicing junction of the same gene; or the at least RNA sequence contains a subsequence substantially identical to an E5 key of an annotated gene, but an immediate downstream sequence of said subsequence is mapped to an intron region of the same annotated gene; or the at least one RNA sequence contains a subsequence substantially identical to an E3 key of a splicing junction, but an immediate upstream sequence of said subsequence is mapped to an intron region of the same annotated gene; or determining that the at least one RNA sequence is a fusion transcript if: the at least one RNA sequence contains a subsequence substantially identical to an E5 key of a first annotated gene, and an immediate downstream sequence of said subsequence is substantially identical to an E3 key of a second annotated gene; or the at least RNA sequence contains a subsequence substantially identical to an E5 key of a first annotated gene, and an immediate downstream sequence of said subsequence is mapped to a second annotated gene; or the at least one RNA sequence contains a subsequence substantially identical to an E3 key of a first annotated gene, and an immediate upstream sequence of said subsequence is mapped to a second annotated gene. 
         [0016]    In some embodiments of the method, the E5 keys, the I5 keys, the E3 keys and the I3 keys in the splicing code table in step (b) have a length of about 20-50 bp. 
         [0017]    In some embodiments of the method, the at least one RNA sequence is obtained from a biochemical analysis such as RT-PCR followed by direct sequencing, RNA sequencing, and transcriptome sequencing (whole-genome RNA sequencing). In some embodiments, the at least one RNA sequence may be retrieved from an online database in which a set of predetermined RNA sequences are deposited. 
         [0018]    In some embodiments, the method for detecting alternatively spliced transcripts or fusion transcripts in RNA sequences may further comprising a quality control step between step (b) and step c), wherein the quality control step comprises removing reads from the at least one RNA sequence, wherein the reads have substantially same sequences as at least one of mitochondrial gene sequences, mitochondrial ribosomal RNA sequences, ribosomal RNA sequences, poly (A) sequences, GC-repetitive sequences, AT-rich sequences, and simple and contaminant sequence reads. 
         [0019]    This method of analyzing RNA sequences for detecting alternatively spliced transcripts or fusion transcripts as disclosed above can be applied to any eukaryotic organism where RNA splicing occurs. Examples of such applications in mammals includes human, mouse or rat. The at least one RNA sequences can be obtained from a biological sample, such as a cell line, a tissue, or a cell-free plasma sample. 
         [0020]    Disclosed herein also includes a method of utilizing knowledge of predetermined fusion transcripts to identify one or more such fusion transcripts from a transcriptome RNA sequencing data obtained from a biological sample, and to then quantitatively determine the expression level of the fusion transcripts in the biological sample. Such a qualitative and quantitative method to characterize at least one RNA sequence read in a transcriptome dataset for fusion transcripts is disclosed, comprising the steps of: 
         [0021]    (a) providing a computer for data identification, aligning, comparison and computation purposes, wherein: the computer has access to the transcriptome dataset, the transcriptome dataset comprising data of genome-wide RNA sequence reads and counts thereof and; and the computer has access to a predetermined fusion transcript table, the predetermined fusion transcript table comprising data of predetermined E5-E3 keys, wherein: each of the predetermined E5-E3 keys corresponds to junction sequence of a predetermined fusion transcript, comprising an E5 key and an E3 key, wherein the E5 key corresponds to a 5′-end subsequence of the predetermined fusion transcript and is mapped to a first annotated gene; the E3 key corresponds to a 3′-end subsequence of the predetermined fusion transcript and is mapped to a second annotated gene; and the E5 key and the E3 key is connected at a junction of the predetermined fusion transcript; 
         [0022]    (b) aligning the at least one RNA sequence read with each of the E5-E3 keys in the predetermined fusion transcript table; and 
         [0023]    (c) determining that the at least one RNA sequence read is mapped to a predetermined fusion transcript if the at least one RNA sequence read contains a subsequence substantially identical to an E5-E3 key in the predetermined fusion transcript table. 
         [0024]    Optionally in some embodiments, the method may further comprise, following step (c), a step of determining expression level of the predetermined fusion transcript to which the at least one RNA sequence read is mapped in the biological sample, the step comprising: (i) determining that E5 key and E3 key of the E5-E3 key, which corresponds to the predetermined fusion transcript, are unique in the transcriptome dataset; and (ii) determining the expression level of the predetermined fusion transcript in the biological sample, by dividing the count of the at least one RNA sequence read by sum of the counts of the genome-wide RNA sequence reads in the transcriptome dataset. 
         [0025]    This disclosure also provides all the fusion transcripts identified by the above mentioned method applied in human cancer cells, with their junction sequences specifically disclosed herein. 
         [0026]    A set of isolated, cloned recombinant or synthetic polynucleotides, is provided herein, comprising at least one polynucleotide, wherein each of the at least one polynucleotide encodes a fusion transcript, the fusion transcript comprising a 5′ portion from a first gene and a 3′ portion from a second gene, wherein the 5′ portion from the first gene and the 3′ portion from the second gene is connected at a junction; the junction has a flanking sequence, comprising a sequence selected from the group of nucleotide sequences as set forth in SEQ ID NOs: 1-258,853, or from complementary sequences thereof. 
         [0027]    Disclosed herein also includes compositions and methods for detecting the presence of the fusion transcripts as disclosed above, based substantially on approaches to detect the above disclosed junction sequences of these fusion transcripts. 
         [0028]    As such, this disclosure provides a composition for detecting, from a biological sample from a subject, the set of polynucleotides which correspond to the above disclosed junction sequences of the fusion genes. 
         [0029]    In some embodiments, the composition may comprise at least one probe, wherein each of the at least one probe comprises a sequence that hybridizes specifically to a junction of a fusion transcript encoded by one of the set of polynucleotides. One such example may include one or more polynucleotide probes for Northern blot analysis to detect the presence of fusion transcripts. Another example may include a plurality of probes, which are immobilized on a substrate and used for microarray analysis to detect the presence of fusion transcripts. 
         [0030]    Yet in some other embodiments, the composition may comprise at least one pair of probes, wherein each of the at least one pair of probes comprises: a first probe comprising a sequence that hybridizes specifically to a first gene of a fusion transcript encoded by one of the set of polynucleotides; and a second probe comprising a sequence that hybridizes specifically to a second gene of the fusion transcript. One example may include one or more pairs of hybridizing probes used in an in situ hybridization (ISH) assay to detect the presence of fusion transcripts. 
         [0031]    Yet in some other embodiments, the composition may comprise at least one pair of amplification primers, wherein each of the at least one pair of amplification primers comprise a first amplification primer comprising a sequence that hybridizes specifically to a first gene of a fusion transcript encoded by one of the set of polynucleotides; a second amplification primer comprising a sequence that hybridizes specifically to a second gene of the fusion transcript; and a means for detecting an amplified product generated between the first amplification primer and the second amplification primer. One example may include a pair of amplification primers used for RT-PCR analysis to detect the presence of fusion transcripts. The composition as such may also comprise a means for generating cDNA molecules from mRNA molecules in the biological sample, such as a reverse transcriptase. 
         [0032]    This disclosure further provides a method for detecting, from a biological sample from a subject, the presence of at least one of the set of polynucleotides which correspond to the above disclosed junction sequences of the fusion genes, comprising: (a) performing a biochemical assay on the biological sample, using at least one gene fusion informative composition for detection of the at least one of the set of polynucleotides; and (b) determining the presence, or absence, of the at least one of the set of polynucleotides in the biological sample. 
         [0033]    In some embodiments of the method, the biochemical assay in step (a) comprises a nucleic acid hybridization technique, such as in situ hybridization (ISH), microarray analysis, and Northern blot analysis. In the embodiment where the biochemical assay in step (a) is a microarray analysis, the biochemical assay may comprise the sub-steps of: (i) isolating mRNA molecules from the biological sample; (ii) converting the mRNA molecules into cDNA molecules, and optionally amplifying the cDNA molecules; (iii) labeling the cDNA molecules; (iv) hybridizing the labeled cDNA molecules to a microarray chip, wherein the microarray chip comprises a plurality of probes and a substrate; the plurality of probes are immobilized on the substrate; and each of the plurality of probes comprises an oligonucleotide sequence that hybridizes specifically to a junction of a fusion transcript encoded by one of the set of polynucleotides; and (v) detecting a pattern of hybridization for each of the plurality of probes. 
         [0034]    Yet in some other embodiments of the method, the biochemical assay in step (a) comprises a nucleic acid amplification technique, selected from the group consisting of: polymerase chain reaction (PCR), reverse transcription polymerase chain reaction (RT-PCR), transcription-mediated amplification (TMA), ligase chain reaction (LCR), strand displacement amplification (SDA), and nucleic acid sequence based amplification (NASBA). In the embodiment where the biochemical assay is reverse transcription polymerase chain reaction (RT-PCR), the biochemical assay in step (a) comprises the sub-steps of: (i) isolating mRNA molecules from the biological sample; (ii) converting the mRNA molecules into cDNA molecules; (iii) performing at least one PCR on the cDNA molecules, using at least one pair of amplification primers, wherein each of the at least one pair of amplification primers comprise a first amplification primer comprising a sequence that hybridizes specifically to a first gene of a fusion transcript encoded by one of the set of polynucleotides; a second amplification primer comprising a sequence that hybridizes specifically to a second gene of said fusion transcript encoded by one of the set of polynucleotides; and (iv) detecting amplification products from the at least one PCR. 
         [0035]    In some embodiments of the method, the biochemical assay in step (a) comprises a nucleic acid hybridization technique, such as in situ hybridization (ISH), microarray analysis, Northern blot analysis, and RNA CaptureSeq. In the embodiment where the biochemical assay is RNA CaptureSeq, the biochemical assay in step (a) comprises the sub-steps of: (i) isolating mRNA molecules from the biological sample; (ii) designing DNA oligonucleotide probes specific to splicing junctions of fusion transcripts; (iii) propagating cDNA libraries; (iv) hybridizing libraries to probes; (v) washing and removing no targeted cDNA; (vi) eluting targeted cDNA for sequencing; and (vi) analyzing captureseq data described above. 
     
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         [0036]      FIG. 1  shows schematic diagram of classification of different types of alternatively-spliced isoforms and fusion transcripts.  1  and  2 ,  3  are upstream, middle and downstream introns. The white, gray and black squares represent upstream, middle and downstream exons, respectively. Reference (REF) is a verified annotated sequence and is used to generate splicing code table. Horizontal arrows indicate alternative splice sites. Vertical arrows indicate junctions of pre-mRNA splicing. A) The sequence is identical to the reference sequence. B) The sequence has no middle exon to form a novel intron. C) The sequence has identical 3′ splice site, but 5′ splice is different from the reference. Splicing generates a 5′ alternatively-spliced isoform. D) The sequence has identical 5′ splice site, but 3′ splice is different from the reference. Pre-mRNA splicing forms a 3′ alternatively-spliced isoform. E) The sequence has both different 5′ and 3′ splice sites. This is a novel intron. F) Two different transcriptional units are originally transcribed separately into different molecules. Genetic alternations have brought two genes together to form a new transcriptional unit and to generate fusion transcripts. Alternatively, trans-splicing generates a fusion transcript. 
           [0037]      FIG. 2  shows schematic procedure of using the splicingcode model to analyze RNA-seq data. The splicingcode program can generate three different tables, which are E5-E3 table, E5 table and E3 table. Using these three tables, we can obtain the most important information of RNA-seq data. The black arrows indicate directions. Horizontal arrows represent two pathways: identification of novel splicing isoforms and discovery of fusion transcripts. 
           [0038]      FIG. 3  shows a detailed description of the method to identify fusion transcripts from RNA-seq reads, shown in the right pathway in  FIG. 2 . 
           [0039]      FIG. 4  shows detailed characterization of the 16,570 fusion transcripts with canonical splice junctions identified from ENCODE from thirty-nine cancer cell line datasets (ECD39). FT and PFG represent fusion transcripts and putative fusion genes supported fusion transcripts, reprehensively. a) Characterization of the fusion transcripts identified from ENCODE thirty-nine cancer cell lines (ECD39). White bar represents total 16,570 fusion transcripts. Some of fusion transcripts are alternatively spliced from the two same putative fusion genes indicated by gray bar. Black bar and gray doted bar represent numbers of 5′ unique genes and 3′ unique genes, respectively. The numbers reduced from total PFG&#39;s numbers indicate 5′ and 3′ gene redundancies, which suggest the numbers of genes can be fused two or more different genes. Dark doted gray bar shows the total numbers of unique genes of both 5′ and 3′ genes, reduction of which indicates a gene can be used as a donor or as an acceptor. Black and gray bars in the Insert of  FIG. 1 a    represent average numbers of sequence reads across splice junctions and average lengths of fusion transcripts, respectively. b) Distribution of fusion transcripts in 39 cancer cell lines. Gray, black, and white bars represent the putative fusion genes, fusion transcripts and the millions of sequence reads used to identify fusion transcripts; c). Type distributions of fusion transcripts. Gray and black bars indicate the putative fusion genes and fusion transcripts, respectively; d). Distributions of cancer cell lines in which fusion transcripts have been identified. Gray, dark gray and black bars represent percentages of fusion transcripts that are detected in 1, 2 and ≧3 cancer cell lines, respectively. 
           [0040]      FIG. 5  shows a Van diagram of overlapped fusion transcripts between different datasets. In this paper, “overlapped” means “identical”. Gray and white circles represent the ECD39&#39;s MCF7 fusion transcripts we have identified and those fusion transcripts validated by Sakarya et al. (Sakarya, et al. 2012). 
           [0041]      FIG. 6  shows Van diagrams of overlapped fusion genes between ECD39 and GCD. a). Van diagram showing identical (overlapped) fusion genes between the ECD39 MCF7 fusion transcripts (dark gray) and the GCD MCF7 fusion transcripts (light gray); b). Van diagram showing identical (overlapped) fusion genes between the total ECD39 fusion transcripts (white circle) and the total GCD fusion transcripts (light gray). 
           [0042]      FIG. 7  shows analysis and characterization of HMGA2|LUM fusion transcripts in osteosarcoma SJSA1 cell line, a multipotential sarcoma. a). Structures of HMGA2 and LUM genes, which are represented by black and gray arrows, respectively. Both genes are on chromosome 12 and separated by 25 Mb. They are brought together by deletions or translocations, which are indicated a pair of paralleled lines. Dashed white box indicates unknown regions between two gens. Black and gray squares represent exons of two different genes while triangle lines represent introns, respectively. Dashed line are omitted exons and introns. Dashed arrow indicates that two genes are close enough to be transcribed into a single molecule pre-mRNA; b) There are two fusion transcripts that differ by two nucleotides (isoform 1 vs isoform 2). c) Expression levels of these two isoforms (isoform 1 vs isoform 2) differ by 4200 folds. 
           [0043]      FIG. 8  shows illustrations and experimental verification of the lowly-expressed CPSF6|CACNA1E fusion transcripts in lymphoblastoid cells GM12878. a). CPSF6 gene on the chromosome 12 and CACNA1E gene on the chromosome 1 have been brought together via translocation indicated by arrows. Black and gray squares represent exons to demonstrate where breakpoints are located on the genes. The numbers indicate exon positions. Solid angle lines and dashed dots represent introns and gaps, respectively. b). RNA-splicing has removed intronic sequences of the putative CPSF6|CACNA1E fusion gene. Black and gray capital letters represent 5′ and 3′ exonic sequences, respectively. Gray and black italic letters represent 5′ and 3′ intronic sequences, respectively. The numbers indicate sequence gaps. c). Diagrams show that the CPSF6|CACNA1E fusion transcript is amplified by RT-PCR. cDNA fragments are then cloned into pCR4-TOPO clone vector. The positive clones are sequenced. The fusion transcripts are verified by blast and visual inspections. Arrow indicates splice junction of the CPSF6|CACNA1E fusion transcripts. Black and gray squares represent CPSF6 exons and CACNA1E exons, respectively. 
           [0044]      FIG. 9  shows analysis and characterization of MTG1|SCART1 (LOC609217) read-through fusion transcripts. a). Schematic diagram of structures of MTG1 and SCART1 genes on the chromosome 10q26.3. The black and dark gray arrows represent MTG1 and SCART1 genes, respectively. Other genes around MTG1 and SCART1 genes are indicated by white and light gray arrows. Dashed lines represent omitted exons and introns. Dashed arrow indicates read-through transcription of a single pre-mRNA molecule, which is spliced into fusion transcript; b) There are eight MTG1|SCART1 fusion transcripts identified, which are shown to be alternatively spliced; The black and gray boxes represent MTG1 and SCART1 exon, respectively. The numbers above the boxes are exon numbers. The numbers in the sequence indicate numbers of omitted nucleotides; c) Distribution of eight MTG1|SCART1 fusion transcripts. Black bars represent the numbers of eight MTG1|SCART1 fusion transcripts detected, respectively. d). Distribution of the total MTG1|SCART1 fusion transcripts detected among different cancer cell lines; and e). Distribution of the normalized MTG1-SCART1 fusion transcripts among different cancer cell lines. Y-axe unit is numbers of transcripts per million sequence reads (NSJMR). 
           [0045]      FIG. 10  shows differential expression of read-through C19orf47|AKT2 fusion transcripts. a). The C19orf47|AKT2 fusion transcripts have been detected in nine normal tissues, which include bone marrow (b. marrow), colon, duodenum, fallopian tubes (f. tube), fat gall bladder (g. bladder), testis, thyroid, tonsil and not found in 20 other tissues including breast and HMEC; b). The C19orf47|AKT2 fusion transcripts have been observed in 9 samples out of 168 HIBCD breast cancer samples. The expressional levels of the C19orf47|AKT2 fusion transcripts are expressed in NSJMR (numbers of splice junctions per million reads). 
           [0046]      FIG. 11  shows analysis of read-through GAL3ST2|NEU4 fusion transcripts. The GAL3ST2|NEU4 fusion transcripts have been found to be expressed only in normal colon tissues, but absent in 26 other tissues and HMEC. This demonstrates that GAL3ST2|NEU4 are differentially expressed. The GAL3ST2|NEU4 fusion transcripts have been detected in 5 different individual cancer tissues. The expressional levels of the GAL3ST2|NEU4 fusion transcripts are expressed in NSJMR (numbers of splice junctions per million reads). 
           [0047]      FIG. 12  shows analysis and characterization of KANSL1 (KIAA1267)|ARL17A fusion transcripts. a). Schematic diagram of structures of ARL17A and KANSL1 genes on the chromosome 17. A potential inversion results in KANSL1-ARL17A gene structure. The gray and black arrows represent the KANSL1 and ARL17A genes, respectively. Dashes arrow indicate potential fusion pre-mRNA; b) there are six KANSL1|ARL17A fusion transcripts identified from cancer cell lines. Black and gray capital letters represent 5′ and 3′ exonic sequences, respectively. The numbers within the sequences indicate the omitted nucleotides; c) Distribution of six KANSL1|ARL17A fusion transcripts detected; d). Distribution of the total KANSL1|ARL17A fusion transcripts among different cancer cell lines; and e). Expression of the normalized KANSL1|ARL17A fusion transcripts among different cancer cell lines. Y-axe unit is numbers of splice junctions per million of sequence-reads (NSJMR). The black and gray boxes represent KANSL1 and ARL17A exons, respectively. Dashed lines indicate omitted exons and introns. The numbers above the boxes are exon numbers. 
           [0048]      FIG. 13  shows an example of using the fusion transcripts&#39; hit maps of fusion transcripts to identify genetic rearrangement hotspots. a). Distribution of total fusion transcripts and inversion fusion transcripts along the chromosome 17. b). Distribution of total fusion transcripts and inversion fusion transcripts found in ≧2 cancer cell lines along the chromosome 17. Each X-axe unit represents 5M bp. Arrows indicate the locations of KANSL1|ARL17A fusion transcripts. The gray triangles and black squares represent total fusion transcripts and inversion fusion transcripts, respectively. 
           [0049]      FIG. 14  shows genome-wide hit maps of fusion transcripts. Relationship between total putative fusion genes (gray triangles) and putative inversion fusion genes whose transcripts existed in two or more cancer cell lines (black squares). a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v and x represent human chromosome 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, and X. Each of X-axe units represents 5 Mb. 
           [0050]      FIG. 15  shows results of comparative analyses of numbers of KANSL1|ARL17A samples between HIBCD and SKBCP datasets. Gray and black squares represent total numbers of samples and the numbers of samples that are found to have KANSL1|ARL17A, respectively. The difference of KANSL1|ARL17A samples between HIBCD and SKBCP is found to be statically significant (p&lt;0.001). 
           [0051]      FIG. 16  shows expressions of KANSL1|ARL17A fusion transcripts in the 168 HIBCD breast cancer samples. X-axe indicates samples&#39; IDs. Y-axe is numbers of splice junctions per million reads (NSJMR). 
           [0052]      FIG. 17  shows results of analysis of the 168 HIBCD (a) and SKBCP (b) breast cancer samples and identification of GABBR1andUBD|PSPH fusion transcripts. a). The GABBR1andUBD|PSPH fusion transcripts have been found in 31 HIBCD samples. b). The GABBR1andUBD|PSPH fusion transcripts have been detected in 7 SKBCP samples. Y-axe is NSJMR. 
           [0053]      FIG. 18  shows verification results of the low-level expressed GABBR1andUBD|PSPH fusion transcripts in breast cancer cell line BT-474. a) GABBR1andUBD gene is located on chromosome 6 and has 24 exons while PSPH genes is on chromosome 7 and has 8 exons. Black and gray squares represent GABBR1andUBD exons demonstrate where breakpoints are located on the genes. Dark and light gray boxes represent PSPH exons to demonstrate where breakpoints are located on the genes. A potential translocation results in putative GABBR1andUBD|PSPH fusion gene, which is represented by black and light gray boxes; b). Black Capital and dark italic gray letters represent exonic and intronic sequences of GABBR1andUBD 5′ splice junction sequences. The light gray italic and gray Capital letters are intronic and exonic sequences of the PSPH 3′ fusion junction; c). These GABBR1andUBD|PSPH fusion transcripts are amplified by RT-PCR. d). RT-PCR fragments are then cloned into pCR4-TOPO clone vector. The positive clones are isolated and sequenced. The arrow indicates splice junctions of the GABBR1andUBD|PSPH fusion transcripts. The black and light gray boxes represent GABBR1andUBD and PSPH exons, respectively. 
           [0054]      FIG. 19  illustrates complex fusion transcripts between non-coding RNA oncogene PVT1 and protein-coding EXOC4 genes. a). A rod-like structure shows that EXOC4 gene is located on Chromosome 7. Gray boxes and black line triangles represent exons and introns, respectively; b). A rod-like structure shows that non-coding RNA PVT1 gene is located on chromosome 8q24 and has been shown to be an non-coding RNA oncogene. The black boxes and triangle lines indicate PVT1 gene structure; c) PVT1|EXOC4 fusion transcripts. 9 fusion transcripts have been identified have been identified in SH-N-SK cancer cell line, a human neuroblastoma. The black and gray rectangle boxes represent the PVT1 and EXOC4 exons, respectively. d) Differential Expression of PVT1|EXOC4 fusion transcripts; e). EXOC4|PVT1 fusion transcripts have been detected in SH—N-SK cancer cell lines. The black and gray rectangle boxes represent the PVT1 and EXOC4 exons, respectively; f) Differential Expression of EXOC4|PVT1 fusion transcripts; g). Expression comparison between EXOC4|PVT1 and EXOC4|PVT1 fusion genes. The gray and black bars represent the PVT1|EXOC4 fusion gene and EXOC4|PVT1 fusion gene, respectively. Y-axe unit is numbers of fusion transcripts. Since these fusion transcripts come from the same dataset, they reflect the differences of these fusion transcript expressions. 
           [0055]      FIG. 20  shows analysis and characterization of non-coding RNA-RNA fusion transcripts. a). The gray and black arrows MEG8 and SNORD114-1 genes respectively. The dashed arrow shows potential inversions or regional duplications of chromosomal 14q32.31 have resulted in inversion of MEG8 and SNORD114-1 gene orders to generate putative SNORD114-1|MEG8 fusion genes; b) Five SNORD114-1|MEG8 fusion transcripts have been detected; c) Distribution of total SNORD114-1|MEG8 fusion transcripts. SNORD114-1|MEG8 fusion transcripts have been detected in seven cancer lines; and d) Distribution of normalized SNORD114-1|MEG8 fusion transcripts in seven cancer lines. Y-axe unit is numbers of transcripts per million sequence reads (NSJMR). The black and gray rectangle boxes represent SNORD114-1 and MEG8 exons, respectively. Here, SNORD114-1 and MEG8 represent abbreviated SNORD114-1andSNORD114-2andSNORD114-3 gene and MEG8andSNORD112andSNORD113-3 gene, respectively. 
           [0056]      FIG. 21  shows results of analysis and characterization of non-coding RNA fusion transcripts. a). Distribution of non-coding RNA fusion transcripts (gray) and PFG (black) among different classes of non-coding RNA fusion transcripts. b) Distribution of -coding RNA fusion transcripts (gray bars) and PFG (black bars) among different cancer cell lines; c) Distribution of different SNHG fusion transcripts. d). Distribution of SNHG3 fusion transcripts among different cancer cell lines; e). Comparison of upstream (gray bars) and downstream (black bars) SNHG fusion transcripts; and f). Comparison of upstream (gray bars) and downstream (black bars) natural networks formed by fusion transcripts. 
           [0057]      FIG. 22  shows diagrams of verification of the lowly-expressed ncRNA00188|GNAI3 fusion transcripts in lymphoblastoid cells GM12878. a). ncRNA00188 gene is located on the chromosome 17 and codes for a non-coding RNA. GNAI3 gene is on the chromosome 1 and a protein-coding gene. Two genes have been brought together via translocation indicated by arrows. Black and gray boxes represent ncRNA00188 exons to demonstrate where breakpoints are located on the ncRNA00188 gene. Black and white boxes represent GNAI3 exons to demonstrate where breakpoints are located on the GNAI3 gene. The numbers indicate above the boxes exon positions. Solid angle lines and dashed dots represent introns and gaps, respectively. b). RNA-splicing has removed intronic sequences of the putative ncRNA00188|GNAI3 fusion gene. Black italic letters and Capital gray letters represent 3′ intronic and 3′ exonic sequences of the GNAI3 splice junction, respectively. The numbers within the sequence indicate sequence gaps. c). Diagrams show that the ncRNA00188|GNAI3 fusion transcript is amplified by RT-PCR. cDNA fragments are then cloned into pCR4-TOPO clone vector. The positive clones are sequenced. The fusion transcripts are verified by blast and visual inspections. Arrow indicates splice junction of the ncRNA00188|GNAI3 fusion transcripts. RT is RT-PCR amplification of GM12878 cDNAs. No products have been detected in other cancer cell lines. M represents DNA markers. 
       
    
    
     BRIEF DESCRIPTION OF THE SEQUENCE LISTING 
       [0058]    The instant disclosure includes a plurality of nucleotide sequences. Throughout the disclosure and the accompanying sequence listing, the WIPO Standard ST.25 (1998; hereinafter the “ST.25 Standard”) is employed to identify nucleotides. The sequences of SEQ ID NOs: 1-258,077 are novel fusion transcripts. The sequences of SEQ ID NOs: 258,078-258,853 may have overlapped with Gene IDs of Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer (Mitelman, et al. 2015). The sequences from SEQ ID NOs: 258,854-259,170 have identical splice junctions to those of the fusion transcripts that have been published. 
       DETAILED DESCRIPTION 
       [0059]    Previously, we have observed that recently-gained human spliceosomal introns have identical 5′ and 3′ splice sites (Zhuo, et al. 2007). Based on this finding, we have found that both 5′ exonic sequences (E5) immediately upstream of introns and 3′ intronic sequences (13) are dynamically conserved and appears rather reminiscent of self-splicing group II ribozymes and of constraints imposed by base pairing between intronic-binding sites (IBSs) and exonic-binding sites (EBSs) (Zhuo, et al. 2012). Therefore, we have proposed that both E5 and 13 sequences constitute splicing codes, which are deciphered by splicer proteins/RNAs via specific base-pairing (Zhuo, et al. 2012). Our splicing code model suggested that a yet-to-be characterized splicer proteins/RNA would decode identical sequences in all pre-mRNAs in conjugation with U snRNAs and spliceosomes, regardless whether the E5 and 13 sequences are in the one molecule or two different molecules. 
         [0060]    In order to generate splicingcode tables, we first and 2010 exons/introns coordinates file are downloaded from the NCBI AceView (ACEVIEW 2010) and the human hg19 genome sequences from UCSC (UCSC 2014). The sequences from the splicing sites have been parsed out by a software program. Generating the human splicing codes have been described in details in U.S. patent application Ser. No. 13/372,180 filed on Feb. 13, 2012 and titled SYSTEM AND METHOD FOR ANALYZING SPLICING CODES OF SPLICEOSOMAL INTRONS. Briefly, we divided 5′ splice site and 3′ splice sites. Starting from the splicing junctions, 5′ splice site are further divided into its 5′ exonic sequence (E5) and 5′ intronic sequence (I5). Similarly, 3′ splice site is divided into 3′ intronic sequence (13) and 3′ exonic sequence (E3). Starting from the splice junction, we scored the length of identical nucleotides (LIN) in an uninterrupted stretch independently for the E5-I3 and I5-E3 alignments. The total LIN of splice sites is sum of the LINs of the E5-I3 and I5-E3 alignments. To increase the quality of fusion transcripts, we removed the introns with LIN≧10 from the splicing codes. Furthermore, we arbitrarily removed all introns with lower-case letters to further improve the quality of fusion transcripts in this study. These two steps reduce to unique introns to 308,854, which are used to measure gene expression. To further reduce redundant E5 and E3 sequences, we only retained introns whose E5 splice sites or E3 splice sites can have maximum of 20 isoforms. Consequently, we reduced the unique E5 sequences to 229,170 and unique E3 sequences to 213,327. 
         [0061]    For the program convenience and clarity, we use the human splicing codes to generate E5-E3 hash tables. Then we use E5-E3 table to generate an E5 table and an E3 table. These three tables have different types of keys, but are associated with a unique ordered value. Selecting the key lengths of the E5-E3 table depends on length of RNA-seq reads. If key lengths are too short, it will put multiple sequences from different genes into on one exon-exon junction. It will increase error if these exon-exon junctions are used to evaluate gene expression patterns. If it is too long, it will increase the quality of the expression data. It may result in less of data points and loss of information especially if lengths of RNA-seq reads are variable. Generally, we have used 20 bp unless they are specified in the context. We have used this E5-E3 table to generate an E5 table and an E3 table. 
         [0062]    In order to be more efficient and accurate to get the most important information of the entire transcriptome, we must correctly identify their splicing junctions. RNA-Seq reads without splicing junctions are less important and contribute a little to their reconstructing genes. Therefore, we will evaluate these RNA-Seq reads further if necessary. In order to get more accurate identification of different classes of splice junctions in RNA-seq datasets, we have selected a well-annotated mRNAs from each gene as reference sequences (REF) shown in  FIG. 1 . RNA-seq sequences are then searched to see whether they have identical E5-E3 junctions or E5 sequences or E3 portions. If they have either E5 or E3 portions, they may be potential novel isoforms or fusion transcripts. Splicing of uncharacterized introns marked by vertical arrows in  FIG. 1  can be classified into following five types of splicing junctions: A) identical introns; B) cassette introns; C) 5′ alternative introns; D) 3′ alternative introns; and E) novel introns. In  FIG. 1F , two transcriptional units or genes may be located on different chromosomes or on different regions of the same chromosome. Inter-chromosomal or intra-chromosomal translocations have brought two transcriptional units close each other to generate a fusion gene, which in turn are transcribed into fusion transcripts. In some other cases, two transcriptional units may be separated by relatively short stretches of sequences (30 Kb-1,000 kb). However, under certain conditions and/or in some tissues, the two transcriptional units are transcribed into one unit to generate fusion transcripts. In other cases, two RNAs from two different molecules are trans-spliced to generate fusion transcripts. 
         [0063]    Since our goal is to generate high-quality data, novel isoforms and fusion transcripts, we have to reduce the most noises first. As shown in  FIG. 2 , in the first step, we have used Quality Control Table to remove mitochondrial gene sequences, mitochondrial ribosomal RNAs, ribosomal RNA sequences, simple sequences, such as poly (A) sequences, GC-repetitive sequences and AT-rich sequences found in the human genomes, and another other sequences, which are thought to be contaminants. To generate Quality Control Table, the selected sequences are used to generate continuous ordered keys. Each key is associated with upstream and downstream sequences, which are used to confirm whether the key is in correct context of the associated sequences. Even though all samples have been rRNA-depleted, we have found that the samples contains up to 20% of ribosomal rRNA sequences and mitochondrial gene sequences. More importantly, we can use this table to remove poor-quality RNA-Seq reads, simple repeat sequences and adaptor sequences. 
         [0064]    If a sequence is found to have a substring present in this E5-E3 hash table, the read&#39;s remaining sequence will be aligned to the corresponding E5 and E3 exonic sequences perfectly or with errors or gaps set by users such as one nucleotide. If the sequence reads match both E5 and E3 sequences from the same splice junctions, these reads will be accounted for gene expression profiling. Otherwise, they are treated as poor-quality reads or as novel transcripts for further analysis. Then we have used both E5 table and E3 table to identify novel alternatively-expressed transcripts and fusion transcripts. 
         [0065]    If RNA-seq reads are mapped into both E5 table and E3 table, but not from the same splice junctions, then they have two different pathways as shown in  FIG. 2 . If both E5 key and E3 key are from the same gene or transcriptional unit (the identical gene ID), they are novel alternative splicing. If both E5 key and E3 key are associated with different gene IDs or transcriptional units, they are potentially fusion transcripts and will be described in detail later. 
         [0066]    If both E5 and E3 keys have the same gene ID and from the same transcription units, then we can check the orders of both E5 key and E3 key to determine types of alternative splicing. 
         [0067]    If a RNA-seq read has been mapped on the same transcriptional unit, there are two or more gaps between the E5 ID value and the E3 ID value. Two more exons have been removed from transcripts. This RNA-seq read is cassette introns as shown by vertical arrow (Type B in  FIG. 1 ). 
         [0068]    The sequence has a subsequence in the E5 table and its immediate downstream sequences are mapped to an E3 key associated with a different value. The transcript sequence is thought to have identical 5′ splice site, but has different 3′ splice site. This sequence is thought to have 3′ alternative splicing as the intron 1 shown in Type C in  FIG. 1 . 
         [0069]    If the transcript is present in the E5 table and length of its downstream sequence is more than the key length, these sequences will be searched by blast to determine the sequence location. If the sequences are located within the downstream gene or downstream sequences of the transcription unit, this sequence is thought to be 3′ alternative splicing. If the sequences are located in another transcription unit, this sequence is thought to be a fusion transcript. 
         [0070]    If the transcript is present in the E3 table and its immediately upstream sequence is more than the key length, these sequences will be searched by blast to determine the sequence location. If the sequences are located within the upstream gene or upstream sequences of the transcription unit, this sequence is thought to be 5′ alternative splicing. If the sequences are located in another transcription unit, this sequence is thought to be a fusion transcript. 
         [0071]    If a RNA-seq read has been mapped to the E3 key, its immediately upstream sequence is mapped to the E5 key with different value. That is, a sequence has identical 3′ splice site with the REF sequence, but has different 5′ splice site, this sequence is thought to have 3′ alternative splicing as shown in Type D in  FIG. 1 . 
         [0072]    If the transcript is present in the E3 table and the length of its upstream sequence is more than the key length, these sequences will be searched by blast to determine the sequence location. If the sequences are located within the upstream gene or upstream sequences of the transcription unit, this sequence is thought to be 5′ alternative splicing. If the sequences are located in another transcription unit, this sequence is thought to be a fusion transcript. 
         [0073]    If the E5 key and E3 key are mapped to keys with different values compared to their REF sequences, this transcript has different 5′ and 3′ splice sites compared to the reference sequence (REF in  FIG. 1 ). The intron 1 of the Type E has been shown to be a novel intron in  FIG. 1 . If the transcript is present in the E3 table and the length of its upstream sequence is more than the key length, these sequences will be searched by blast to determine the sequence location. If the sequences are located within the upstream gene or upstream sequences of the transcription unit, this sequence is thought to be 5′ alternative splicing. If the sequences are located in another transcription unit, this sequence is thought to be a fusion transcript. 
         [0074]    In order to assemble the transcriptome and to characterize novel and unpredictable transcriptional events, we have added middle exon table in this RNA-seq analysis program. To generate the middle exon table, we have adopted one of two strategies deepening on the computer system memories and lengths of RNA-seq reads: continuous non-redundant and unique keys or gapped (normally less than half of the key length) non-redundant and unique keys. RNA-seq reads are mapped into the middle exon table. 
         [0075]    To measure the gene expression, we have adopted splice junction centered strategy. That is, we would count the sequence reads covering splice junctions and ignore all other parts of mRNA sequences. We first selected the human 308,854 splice junctions from human Aceview 37 genes from 382,279 distinct exon/intron junction sequences as described above. As described above, we removed the introns with LIN ≧10 from the splicing codes. We arbitrarily removed all introns with lower-case letters to further improve the quality of fusion transcripts in this study. These two steps reduce to unique introns to 308,854, which are used to measure gene expression. We have combined 20 bp E5 and 20 bp E3 key sequences as unique splice junction database. RNA-seq reads are searched against this human splice junction database. If a sequence read contain sequences in the splice junction database, this splice junction is counted. To be consistent with identification of fusion transcripts, we allow no mismatches. To quantify gene expression levels, we summed the total numbers of sequence reads per gene. The numbers of the splice junctions we have identified are divided by the sums of sequence reads. The results are expressed in Numbers of Splice Junction per Million mapped Reads (NSJMR). 
         [0076]    In order to measure expression of the fusion transcripts identified so far, we have adopted a strategy similar to measure gene expression described above. We have divided the fusion transcripts into E5 and E3 sequences from fusion junctions as described above. We have taken a substring of an E5 sequence as the E5 key and a substring of an E3 sequence as E3 key. Both E5 and E3 keys of the same fusion transcripts are combined together to form a join key of a fusion transcript. The length of each of both E5 and E3 keys are at least 20 bp to make sure that the joint key will be unique in a transcriptome. If a sequence contains this joint key, this sequence is counted as a fusion transcript, the numbers of this fusion transcript are summed together in a dataset. The numbers of the fusion junctions we have identified are divided by the sums of sequence reads of the dataset. The results are expressed in Numbers of Splice Junction per Million mapped Reads (NSJMR). 
         [0077]    As shown in  FIG. 2 , when a sequence read is mapped to E5 table and its immediately downstream key is mapped to an E3 key of different gene, this sequence read is thought to be a putative fusion transcript. Due to enormous importance of fusion transcripts, we have given more detailed description to discover fusion transcripts in  FIG. 3 . After we have found that a sequence have both E5 and E3 keys on different genes, we will further check whether 5′ RNA-seq read sequences have identical sequences upstream of the E5 key sequence and if 3′ remaining read sequence match an identical sequence downstream of the E3 key sequences. If a read sequence has identical E5 and E3 sequences from two different genes, this read sequence are further checked by BLAST against the mRNA database to see if they come from pseudogenes or from gene duplications or from alternative splicing. If the RNA-seq read doesn&#39;t originate from one single transcription unit, this fusion sequence is searched against E5 and E3 gene sequences via gene hash tables to rule out whether the fusion transcript comes from alternative splicing. The entire identification process of fusion transcripts has used zero tolerance of errors in this study. The fusion transcripts have been randomly selected and verified by manual inspections. In addition, the fusion transcripts are systematically BLASTed against AceView mRNA sequences and BLASTed against human genes parsed from human hg19 genome sequences to make sure that each of the fusion transcripts originates from two different genes. 
         [0078]    To use the splicing code to identify fusion transcripts, a computation system used three steps: 1) mapping a sequence read to 20 bp 5′ (E5) and 20 bp 3′ (E3) exonic sequences of canonical splice-sites of two different transcription units; 2) aligning remaining sequences to corresponding upstream and downstream regions; and 3) removing alternatively-spliced false positive sequences from one transcription unit by blast against mRNA and gene databases. These steps have shown that splicing code table is the key to determine qualities of fusion transcripts. We have downloaded AceView-NCBI-37 genes, which contain 382, 279 distinct introns (Thierry-Mieg and Thierry-Mieg 2006). After removing introns from intergenic regions and E5 or E3 sequences whose frequencies are larger than 20, the table contained 221,970 E5 sequences and 213,327 E3 sequences, respectively. A sequence is mapped to E5 and E3 keys from two different genes. Then, the upstream sequence of the E5 key and the downstream of the E3 key are aligned to the corresponding genomic regions, respectively. If they are identical, this sequence is thought to be a fusion transcript. Consequently, our system would greatly reduce randomly generated false positive sequences, but also remove some true fusion transcripts. The maximum random error to generate a fusion transcript is 1.2×10 −24  and the medium error is 1×10 −59 . 
         [0079]    Using this computation system, first we have analyzed 37,208 millions of RNA-seq reads from thirty-nine cancer lines, majorities of which are downloaded from ENCODE project (ENCODE 2015). RNAs data sizes range from 31 millions of MDA-MB-231 to 6945 millions of MCF-7. For convenience, we have assigned these 16,570 fusion transcripts as Encode Cancer 39 Datasets (ECD39 Dataset) (ENCODE 2015). After we have analyzed ECD39 fusion transcripts and obtained summary information of the total fusion transcripts. 
         [0080]    We have further downloaded four colon cancer datasets, two breast cancer datasets, two lung cancer data and normal tissues and primary cell lines (ENCODE 2015, SCILIFELAB 2015). 
         [0081]    After we completed analyses of ECD39, we have continued analyzing the other cancer datasets downloaded from NCBI (ENA 2014) and ENA (ENA 2014). So far, we have identified total of 259, 170 fusion transcripts with unique canonical splice sites and represent 242,578 putative fusion genes. Then, we have downloaded the information from four large fusion transcripts, which include TCGA Fusion genes (Yoshihara, et al. 2014), Genentech&#39;s cancer fusion genes (Klijn, et al. 2015), Life Technology′ breast cancer fusion transcripts (Sakarya, et al. 2012) and Mayo Clinic Rochester&#39;s breast cancer fusion genes (Asmann, et al. 2012). We have parsed out &gt;14,000 fusion transcripts from these fusion gene data. We have shown that 317 transcripts out of 253,747 fusion transcripts have identical fusion junctions. Next, we have compared our unique IDs with Mitelman Cancer Fusion Gene Database (Mitelman, et al. 2015), which contains 10,004 fusion genes so far. We have identified 776 fusion transcripts, whose Gene IDs are overlapped with those from Mitelman Cancer Fusion Gene Databases (Mitelman, et al. 2015). These have demonstrated that most of the fusion transcripts are novel and unique. Since the majorities of 39 cancer cell lines are from ENCODE projects (Table 1), their data handling and experimental error controls are uniforms. Because of these properties and characteristics of ENCODE datasets, it has made us much easier to remove mistakes and errors. The conclusions have been much reliable and reproducible. Therefore, our discussion will focus on this subset of datasets. 
         [0082]    After we have performed analyses of the ENCODE RNA-seq datasets, we have discovered 92,817 fusion transcripts from these thirty-nine RNA-seq data, which represents 36.6% of the total fusion transcripts. In order to be more efficient to characterize the fusion transcripts, we have used them to analyze and dissect characteristics of fusion transcripts in more details and the other fusion transcripts are presented in the context of discussions, we have indentified 16,570 subset of fusion transcripts, which are supported by at least three sequences across the splice junction by minimum 40 bp (at least 20 bp at each of fusion transcripts) or by at least two alternatively-spliced fusion transcripts of the same two genes. For convenience, we have assigned these 16,570 fusion transcripts as Encode Cancer 39 Fusion Transcript Data (ECD39). 
         [0083]    Table 1 has shown list of the thirty-nine cancer cell lines in the ECD39 datasets, the numbers of fusion transcripts (FT), the numbers of putative fusion genes (PFG), and the numbers of RNA-seq reads used for analyses. 
         [0000]    
       
         
               
             
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 The information of the thirty-nine cancer cell lines (ECD39) 
               
               
                 and their fusion transcripts identified. FT and PFG represent 
               
               
                 fusion transcripts and putative fusion genes, respectively. 
               
             
          
           
               
                 Cancer Cell Lines 
                 # of FT 
                 # of PFG 
                 # of Million Reads 
               
               
                   
               
             
          
           
               
                 A172 
                 190 
                 186 
                 393 
               
               
                 A375 
                 375 
                 362 
                 445 
               
               
                 A431 
                 263 
                 244 
                 409 
               
               
                 A549 
                 2053 
                 1765 
                 1933 
               
               
                 Caki2 
                 146 
                 142 
                 447 
               
               
                 CUTLL 
                 554 
                 455 
                 462 
               
               
                 Daoy 
                 226 
                 219 
                 393 
               
               
                 G401 
                 91 
                 90 
                 398 
               
               
                 H4 
                 216 
                 213 
                 390 
               
               
                 H460 
                 378 
                 357 
                 849 
               
               
                 HCC1599 
                 442 
                 387 
                 230 
               
               
                 HCT116 
                 422 
                 403 
                 498 
               
               
                 Hela-3 
                 1177 
                 1025 
                 1977 
               
               
                 HepG2 
                 2377 
                 1886 
                 5116 
               
               
                 HT1080 
                 446 
                 441 
                 391 
               
               
                 HT29 
                 392 
                 382 
                 465 
               
               
                 K562 
                 3374 
                 2572 
                 3683 
               
               
                 Karpas422 
                 211 
                 205 
                 293 
               
               
                 KATOIII 
                 128 
                 111 
                 186 
               
               
                 LHCN-M2 
                 860 
                 768 
                 1391 
               
               
                 LIM1899 
                 327 
                 283 
                 216 
               
               
                 LIM2405 
                 87 
                 76 
                 248 
               
               
                 M059J 
                 206 
                 203 
                 327 
               
               
                 MCF7 
                 2315 
                 1763 
                 6945 
               
               
                 MDA-MB 
                 114 
                 105 
                 31 
               
               
                 MG63 
                 149 
                 147 
                 304 
               
               
                 OCI-Ly7 
                 342 
                 332 
                 309 
               
               
                 PC3 
                 317 
                 311 
                 437 
               
               
                 REC1 
                 465 
                 403 
                 258 
               
               
                 RPMI-7951 
                 420 
                 406 
                 345 
               
               
                 SJCRH30 
                 565 
                 530 
                 380 
               
               
                 SJSA1 
                 251 
                 242 
                 388 
               
               
                 SK-Mel-5 
                 300 
                 294 
                 413 
               
               
                 SK-N-DZ 
                 826 
                 799 
                 1131 
               
               
                 SK-N-SH 
                 1731 
                 1445 
                 4622 
               
               
                 SUN16 
                 55 
                 47 
                 138 
               
               
                 U251 
                 33 
                 33 
                 110 
               
               
                 U2OS 
                 21 
                 20 
                 102 
               
               
                 U87 
                 148 
                 130 
                 158 
               
               
                   
               
             
          
         
       
     
         [0084]    The ECD39 fusion transcripts have 16,570 fusion transcripts with canonical splice junctions which, on average, are supported by 8.9 copies of sequence reads and are 98 bp long ( FIG. 4 a    Insert). These fusion transcripts represent 11,488 unique combinations of putative fusion genes (PFGs) ( FIG. 1 a   ). On average each PFG have 1.44 fusion transcript isoforms. This suggests that PFGs are similar to annotated genes, which have complex alternatively-spliced isoforms.  FIG. 4 a    shows that 11,488 PFGs have 5705 unique 5 ‘-genes and 5606 unique 3’-genes, respectively, which indicate that each 5′ or 3′ gene could form two different PFGs ( FIG. 4 a   ). The total 11488 PFGs have 8229 unique genes, 39% of which are involved in both 5′ and 3′ gene fusion ( FIG. 4 a   ). These data are consistent with previous findings that fusion events are recurrent in cancer. To evaluate origins of the fusion transcripts, we have analyzed distributions of the fusion transcripts among 39 cell lines. The numbers of fusion transcripts identified range from 21 in U2OS to 3374 in K562, lymphoblast of chronic myelogenous leukemia ( FIG. 4 b   ). Even though larger data result in more numbers of fusion transcripts, there is no direct correlation among them. Among eight cell lines that have &gt;1,000 million RNA-seq reads, A549, adenocarcinomic human lung epithelial cells, have 1.06 numbers of splice sites per million reads (NSJMR) while MCF-7 and SK-N-SH have 0.33 and 0.38 NSJMR, which may partly reflect characteristics of cancer types. 
         [0085]    To systematically characterize properties of these ECD39 fusion transcripts, we have arbitrarily classified these fusion events into five groups based on locations, orientations and distances between two genes: inter-chromosomal translocations, intra-chromosomal translocations, inversions, deletions, and read-through. These five genetic types of the fusion transcripts are defined as below. If 5′ and 3′ regions of a fusion transcript originate from two different chromosomes, this fusion transcript is thought to be inter-chromosomal translocation. If 5′ and 3′ regions of a fusion transcript are from the same chromosome and the distances between two regions are more than 1 million by in length, this fusion transcript is defined as the intra-chromosomal translocation. If 5′ and 3′ regions of a fusion transcript come from the same chromosome and the distances between two regions are larger than 1 million by in length and the both 5′ and 3′ regions are on the same strands, this fusion transcript is defined as the deletion. If 5′ and 3′ regions of a fusion transcript come from the same chromosome and the distances between two regions are less than 1 million by in length but 5′ and 3′ regions are the opposite strands, this fusion transcript is an inversion. If 5′ and 3′ regions of a fusion transcript come from the same chromosome and the distances between two regions are less than 1 million by in length and 5′ and 3′ regions are the same strands, this fusion transcript is thought to be read-through. 
         [0086]      FIG. 4 c    shows that inter-chromosomal transcripts and FPGs are the highest among the five groups and accounted for 40% and 51%, while the deletion transcripts and PFGs are the lowest and count for 4.6% and 4.1% respectively. As Table 2 shows, inter-chromosomal translocation, intra-chromosomal translocation and deletion transcripts, whose gaps between two genes are ≧1 million bp, have very low fusion transcripts per PFG and ranged from 1.13 to 1.31. On the other hand,  FIG. 4 c    has shown that the read-through and inversion transcripts, whose gaps between two genes are ≦1 million bp, have the most fusion transcripts per PFG, which are 2.22 and 1.86, respectively. That the fusion transcripts per PFG of read-though and inversion are much larger than those of inter-chromosomal translocation, intra-chromosomal translocation and deletion suggests that numbers of transcripts per PFG are associated with the gap sizes between two genes. Since the read-through genes are more like traditional genes, inter-chromosomal, intra-chromosomal and deletion fusion genes may have some mechanisms different from the “traditional” ones to generate fusion transcripts. Because identification of recurrent fusion transcripts among different types of cancer is extremely important for cancer diagnosis, therapy and prognosis, we have analyzed the recurrent fusion transcripts among the different groups of cancer cell lines. 
         [0087]    To characterize the differences between the splicingcode method and other methods to identify fusion transcripts, we use the human multiple cancer types dataset (named as HMCT) from Stanford University (Giacomini, et al.). The HMCT dataset has seven samples, which have been generated by two types of sequence machines: Illuminia HiSeq 2000 and Genome Analyzer II. The four samples analyzed by Genome Analyzer II have 35 bp RNA-seq reads in length and three samples by Illuminia HiSeq 2000 have 100 bp RNA-seq reads. Due to short sequences lacking specificities, we have to discard four samples with shorter 35 bp sequences from further analysis. We have performed data analysis of three samples by Illuminia HiSeq 2000 and have identified 2205 fusion transcripts, four of which have been validated by Giacomini et al (Giacomini, et al. 2013). 
         [0088]    Compared to other methods, we have less copy numbers of supporting RNA-seq reads per fusion transcript. We have analyzed the numbers of supporting sequence reads. Table 2 shows differences of supported sequence reads among the four genes uncovered by splicingcodes and validated by Giacomini et al (Giacomini, et al. 2013). From Table 2, the four genes have an average of the HMCT 54.7 sequence reads while they are supported by 7.5 sequence reads in our splicingcodes model, which are 7.5 folds less than the former. Table 2 shows that the BCL6|RAF1 fusion transcript has been supported by 39 HMCT reads and 2 SplicingCodes reads, respectively. This is almost 20 fold differences. This has demonstrated that splicingcodes model has used 
         [0000]                                                                                  TABLE 2                   Differences of numbers of supported reads                5′ Genes   3′ Genes   HMCT   SplicingCodes                            BCL6   RAF1   39   2           FAM133B   CDK6   30   10           EWSR1   CREM   120   14           ABL1   CBFB   30   4                Average   54.75   7.5                        
much stringent conditions.
 
         [0089]    As shown in Table 1 and  FIG. 4 b   , we have identified 2315 fusion transcripts with unique canonical splice sites, which represent 1763 unique putative fusion genes. Since MCF7 has been well-studied in transcriptional studies, it is natural for the MCF7 fusion transcripts from two different studies should have common identical fusion transcripts. Sakarya et al. have used a suffix array algorithm to analyze a MCF7 RNA-seq dataset and identified 40 and validated novel fusion genes (Sakarya, et al. 2012).  FIG. 5  has shown the Van diagram between our fusion transcripts and those identified and validated by Sakarya et al (Sakarya, et al. 2012). Even though our datasets contain no MCF-7 RNA-seq datasets used by Sakarya et al., we have found that 31 (75%) of fusion transcripts are identical with those identified by Sakarya et al. (Sakarya, et al. 2012). 
         [0090]    To further evaluate the quality of our fusion gene detection method, we have performed analysis on our ECD39 MCF7 fusion transcripts, which have MCF-7 2315 fusion transcripts representing 1763 fusion genes. Then, we parse out 132 GCD MCF7 fusion transcripts from the GCD datasets (Klijn, et al. 2015).  FIG. 6 a    has shown that the ECD39&#39;s MCF7 fusion transcripts have been shown to have 49 (39.9%) genes overlapped with GCD MCF-7 132 fusion genes. Based on numbers of supporting reads, we can conclude that the fusion transcripts majorities of which are highly expressed. This strongly supports that our method is highly accurate. 
         [0091]    To further characterize fusion transcripts, we have compared our data with large scale identification of 5451 fusion transcripts from 675 human cancer cell lines by Klijin et al. (referred as Genetech Cancer Data (GCD)) (Klijn, et al. 2015). Compared to the total GCD fusion transcripts,  FIG. 6 b    shows that our ECD39 fusion transcripts have been found to have only identified 276 fusion transcripts, whose gene IDs are overlapped with GCD fusion genes, which count for 1.7%. Since the GCD fusion transcripts originated from 675 human cancer cell lines (Klijn, et al. 2015), there are eight cell lines overlapped between two datasets. Only small numbers of overlapped transcripts between two datasets of fusion transcripts have further confirmed that cancer is heterogeneous. 
         [0092]    Reviewing identical fusion transcripts have shown that these fusion genes have been highly expressed based on the numbers of supporting sequence reads. It seems that all methods of identification of fusion transcripts are able to identify the highly-expressed fusion transcripts. However, our method identifies highly-expressed fusion transcripts, but also very lowly-expressed fusion transcripts. 
         [0093]    In  FIG. 4 b   , we have classified the fusion transcripts based on the ECD39 cell line types. Table 3 shows lists of the top ten fusion transcripts of the thirty-nine cancer cell lines. 
         [0000]    
       
         
               
             
               
               
               
               
             
               
             
               
               
               
               
             
               
             
               
               
               
               
             
               
             
               
               
               
               
             
               
             
               
               
               
               
             
               
             
               
               
               
               
             
               
             
               
               
               
               
             
               
             
               
               
               
               
             
               
             
               
               
               
               
             
               
             
               
               
               
               
             
               
             
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 The top ten highly-expressed fusion transcripts in each of the 
               
               
                 ECD39 thirty-nine cancer cell lines. Underlined gene symbols 
               
               
                 represent a transcriptional unit of multiple gene complexes. 
               
             
          
           
               
                 Cell Lines 
                 5 Gene 
                 3 Gene 
                 Counts 
               
               
                   
               
             
          
           
               
                 Table 3a Top ten highly-expressed fusion 
               
               
                 transcripts of A172, A375, A431 and A562 
               
             
          
           
               
                 A172 
                 CNOT1 
                 ARHGAP17 
                 137 
               
               
                 A172 
                 SNTB2andVPS4A 
                 IL34 
                 130 
               
               
                 A172 
                 NSD1 
                 DHX15 
                 85 
               
               
                 A172 
                 PIKFYVE 
                 ACTL6A 
                 77 
               
               
                 A172 
                 URB1 
                 SLC27A1 
                 70 
               
               
                 A172 
                 SMC4 
                 TAF9 
                 69 
               
               
                 A172 
                 ABL1 
                 CBFB 
                 64 
               
               
                 A172 
                 DUSP14 
                 DDX52 
                 60 
               
               
                 A172 
                 ALPK2 
                 ARID4BandRBM34 
                 56 
               
               
                 A172 
                 METTL9 
                 SDK1 
                 52 
               
               
                 A375 
                 KIAA1267 
                 ARL17AandARL17B 
                 60 
               
               
                 A375 
                 ST3GAL2 
                 COG4 
                 48 
               
               
                 A375 
                 ALDH1A3 
                 CALM2andC2orf61 
                 36 
               
               
                 A375 
                 HIF1AandSNAPC1 
                 PRKCH 
                 31 
               
               
                 A375 
                 ETV5 
                 TRA2B 
                 28 
               
               
                 A375 
                 C5orf30 
                 SYNCRIP 
                 26 
               
               
                 A375 
                 TPM4 
                 SUN1andGET4 
                 25 
               
               
                 A375 
                 PPP3CA 
                 HDGFRP3 
                 24 
               
               
                 A375 
                 BAGE 
                 BAGE3 —   
                 24 
               
               
                 A375 
                 MAP2K5 
                 SKOR1andPIAS1 
                 23 
               
               
                 A431 
                 TPX2 
                 C20orf112 
                 24 
               
               
                 A431 
                 PRIM1 
                 NACA 
                 21 
               
               
                 A431 
                 ZNF782 
                 ZNF510 
                 19 
               
               
                 A431 
                 EGFR 
                 PPARGC1A 
                 14 
               
               
                 A431 
                 LOC283299 
                 OVCH2 
                 10 
               
               
                 A431 
                 EXOC4 
                 CHCHD3 
                 10 
               
               
                 A431 
                 NRIP1 
                 LOC100128341 
                 8 
               
               
                 A431 
                 SLC38A1 
                 SRSF2IP 
                 8 
               
               
                 A431 
                 FAM18B2andCDRT4 
                 TEKT3 
                 8 
               
               
                 A431 
                 CLTC 
                 TMEM49 
                 8 
               
               
                 A549 
                 MFGE8 
                 HAPLN3 
                 468 
               
               
                 A549 
                 SCAMP2 
                 WDR72 
                 411 
               
               
                 A549 
                 KIAA1267 
                 ARL17AandARL17B 
                 212 
               
               
                 A549 
                 C19orf47 
                 AKT2 
                 139 
               
               
                 A549 
                 UBA2 
                 WTIP 
                 133 
               
               
                 A549 
                 P2RY6 
                 ARHGEF17 
                 112 
               
               
                 A549 
                 NCEH1 
                 MUC13 
                 78 
               
               
                 A549 
                 ACCS 
                 EXT2 
                 73 
               
               
                 A549 
                 MFGE8 
                 HAPLN3 
                 64 
               
               
                 A549 
                 ST6GALNAC4 
                 ST6GALNAC6andAK1 
                 53 
               
             
          
           
               
                 Table 3b Top ten highly-expressed fusion 
               
               
                 transcripts of CUTLL, Caki2, Daoy and G401 
               
             
          
           
               
                 CUTLL 
                 TRBV —   
                 NOTCH1 
                 534 
               
               
                 CUTLL 
                 LZTFL1 
                 SLC6A20 
                 200 
               
               
                 CUTLL 
                 THEMIS 
                 PTPRK 
                 41 
               
               
                 CUTLL 
                 C6orf106 
                 LOC100132288 
                 34 
               
               
                 CUTLL 
                 SLC35A3 
                 HIAT1 
                 32 
               
               
                 CUTLL 
                 TRBV —   
                 NOTCH1 
                 30 
               
               
                 CUTLL 
                 UBA2 
                 WTIP 
                 24 
               
               
                 CUTLL 
                 ZNF782 
                 ZNF510 
                 24 
               
               
                 CUTLL 
                 ERBB2IP 
                 SFRS12 
                 19 
               
               
                 CUTLL 
                 PSMA4 
                 CHRNA5 
                 17 
               
               
                 Caki2 
                 MICALL1 
                 POLR2F 
                 524 
               
               
                 Caki2 
                 PKD1 
                 NTHL1 
                 201 
               
               
                 Caki2 
                 DLG5 
                 TPH1andSERGEF 
                 158 
               
               
                 Caki2 
                 TSSC1 
                 KIDINS220 
                 145 
               
               
                 Caki2 
                 TUSC3 
                 EXOC6B 
                 135 
               
               
                 Caki2 
                 PCMT1 
                 PDSS2 
                 127 
               
               
                 Caki2 
                 MED26 —   
                 ZBTB1 
                 115 
               
               
                 Caki2 
                 C6orf105 
                 ZCCHC11 
                 103 
               
               
                 Caki2 
                 CELSR1 
                 TMCO3 
                 82 
               
               
                 Caki2 
                 AGPS 
                 VAPA 
                 76 
               
               
                 Daoy 
                 TM7SF3 
                 C12orf11 
                 164 
               
               
                 Daoy 
                 KIF5B 
                 ZEB1 
                 132 
               
               
                 Daoy 
                 ALCAM 
                 ACTR3 
                 69 
               
               
                 Daoy 
                 GNB2L1 —   
                 ADPRHL2 
                 65 
               
               
                 Daoy 
                 ZNF782 
                 ZNF510 
                 64 
               
               
                 Daoy 
                 RC3H2 
                 KATNA1 
                 62 
               
               
                 Daoy 
                 YIPF4 
                 DYM 
                 60 
               
               
                 Daoy 
                 G3BP1 
                 ANXA2 
                 58 
               
               
                 Daoy 
                 LEPROTL1 
                 INTS9 
                 56 
               
               
                 Daoy 
                 FNBP1 
                 GTF2IRD2B 
                 53 
               
               
                 G401 
                 LOC283299 
                 OVCH2 
                 74 
               
               
                 G401 
                 HRSP12 
                 GDI2 
                 69 
               
               
                 G401 
                 CLN6andCALML4 
                 GABRA5 
                 55 
               
               
                 G401 
                 MLL3 
                 BAGE3 —   
                 45 
               
               
                 G401 
                 MTHFD2 
                 MOBKL1B 
                 44 
               
               
                 G401 
                 GDPD5 
                 CHD8 
                 38 
               
               
                 G401 
                 PRDX2 
                 GNAS 
                 37 
               
               
                 G401 
                 LOC728190 
                 GLUD1 
                 36 
               
               
                 G401 
                 TBC1D30 
                 MSRB3 
                 32 
               
               
                 G401 
                 DCUN1D2 
                 LAMP1 
                 26 
               
             
          
           
               
                 Table 3c Top ten highly-expressed fusion 
               
               
                 transcripts of H4, H460, HCC1599 and HCT116 
               
             
          
           
               
                 LHCN-M2 
                 ZNF782 
                 ZNF510 
                 91 
               
               
                 LHCN-M2 
                 EEF1DP3 
                 FRY 
                 69 
               
               
                 LHCN-M2 
                 TBC1D23 
                 NIT2 
                 30 
               
               
                 LHCN-M2 
                 MICAL3 
                 BCL2L13 
                 28 
               
               
                 LHCN-M2 
                 ADAM9 
                 ADAM32 
                 27 
               
               
                 LHCN-M2 
                 ZBED5 —   
                 KIAA0319L 
                 25 
               
               
                 LHCN-M2 
                 SLC7A5P2 
                 LOC641298 
                 25 
               
               
                 LHCN-M2 
                 NRIP1 
                 LOC100128341 
                 23 
               
               
                 LHCN-M2 
                 CTNNA1 
                 SIL1 
                 21 
               
               
                 LHCN-M2 
                 WLS 
                 DIRAS3 
                 19 
               
               
                 LIM2405 
                 VAX2 
                 ATP6V1B1 
                 5 
               
               
                 LIM2405 
                 SUMO2 
                 HN1 
                 3 
               
               
                 LIM2405 
                 ACCS 
                 EXT2 
                 3 
               
               
                 LIM2405 
                 CHCHD2 
                 PHKG1 
                 3 
               
               
                 LIM2405 
                 NRIP1 
                 LOC100128341 
                 2 
               
               
                 LIM2405 
                 XK 
                 CYBB 
                 2 
               
               
                 LIM2405 
                 ACCS 
                 EXT2 
                 2 
               
               
                 LIM2405 
                 SLC35A3 
                 HIAT1 
                 2 
               
               
                 LIM2405 
                 XK 
                 CYBB 
                 1 
               
               
                 LIM2405 
                 ZW10 
                 TMPRSS5 
                 1 
               
               
                 LIM1899 
                 UHRF1BP1L 
                 ANKS1B 
                 102 
               
               
                 LIM1899 
                 CDK13 
                 C7orf10 
                 14 
               
               
                 LIM1899 
                 MIR17HG 
                 GPC5 
                 12 
               
               
                 LIM1899 
                 ARNTL 
                 MICAL2 
                 9 
               
               
                 LIM1899 
                 UHRF1BP1L 
                 ANKS1B 
                 9 
               
               
                 LIM1899 
                 SLC35A3 
                 HIAT1 
                 8 
               
               
                 LIM1899 
                 LOC389641 
                 CHMP7 
                 7 
               
               
                 LIM1899 
                 ZNF619andZNF620 
                 ZNF621 
                 6 
               
               
                 LIM1899 
                 PLEKHM1P 
                 LOC146880 
                 5 
               
               
                 LIM1899 
                 UBA2 
                 WTIP 
                 5 
               
               
                 M059J 
                 SLC23A2 
                 RNF130 
                 51 
               
               
                 M059J 
                 NLGN1 
                 IFI6 
                 46 
               
               
                 M059J 
                 PRSS23 
                 PSMB2 
                 41 
               
               
                 M059J 
                 CPSF6 
                 ZNF532 
                 35 
               
               
                 M059J 
                 CYLD 
                 PHKB 
                 34 
               
               
                 M059J 
                 CCBL2 
                 MYO19 
                 33 
               
               
                 M059J 
                 KIAA1267 
                 ARL17AandARL17B 
                 31 
               
               
                 M059J 
                 HDAC8 
                 CITED1 
                 30 
               
               
                 M059J 
                 SIKE1andCSDE1andNRAS 
                 ZNF148andSLC12A8 
                 29 
               
               
                 M059J 
                 FLJ34690 
                 MYOCD 
                 26 
               
             
          
           
               
                 Table 3d Top ten highly-expressed fusion 
               
               
                 transcripts of HT1080, HT29, Karpas422 and KATOIII 
               
             
          
           
               
                 HT1080 
                 YWHAQ 
                 LPIN1 
                 36 
               
               
                 HT1080 
                 WDFY1andAP1S3 
                 SERPINE2 
                 32 
               
               
                 HT1080 
                 FBXO34 
                 FOXN3 
                 27 
               
               
                 HT1080 
                 GAS6 
                 TFDP1 
                 26 
               
               
                 HT1080 
                 KCNH5 
                 HIF1AandSNAPC1 
                 26 
               
               
                 HT1080 
                 UBE2S 
                 ACTN4 
                 25 
               
               
                 HT1080 
                 BRIX1 
                 DPY19L4 
                 25 
               
               
                 HT1080 
                 DYNC1H1 
                 PPP2R5C 
                 25 
               
               
                 HT1080 
                 CALN1 
                 HS3ST3B1 
                 24 
               
               
                 HT1080 
                 ECSITandZNF653 
                 PRKCSH 
                 23 
               
               
                 HT29 
                 MTMR3 
                 APOH 
                 488 
               
               
                 HT29 
                 USP6NL 
                 UPF2 
                 269 
               
               
                 HT29 
                 KIAA1267 
                 ARL17AandARL17B 
                 194 
               
               
                 HT29 
                 UBA2 
                 WTIP 
                 79 
               
               
                 HT29 
                 RPL23AP5 
                 NME4andDECR2 
                 78 
               
               
                 HT29 
                 EEF1DP3 
                 FRY 
                 60 
               
               
                 HT29 
                 C11orf9 
                 FAM132A 
                 53 
               
               
                 HT29 
                 PAWR 
                 NAP1L1 
                 53 
               
               
                 HT29 
                 TRA2B 
                 RABGAP1andGPR21 
                 45 
               
               
                 HT29 
                 PAOXandMTG1 
                 LOC619207 
                 44 
               
               
                 Karpas422 
                 KIAA1267 
                 ARL17AandARL17B 
                 271 
               
               
                 Karpas422 
                 HNRNPA1L2 
                 EXOC4 
                 82 
               
               
                 Karpas422 
                 DCAF16andFAM184B 
                 PHF14 
                 66 
               
               
                 Karpas422 
                 LOC100288132 
                 TRMT1 
                 41 
               
               
                 Karpas422 
                 RPL23AP5 
                 NME4andDECR2 
                 40 
               
               
                 Karpas422 
                 PLEKHM1P 
                 LOC146880 
                 36 
               
               
                 Karpas422 
                 EPN1 
                 BPTF 
                 30 
               
               
                 Karpas422 
                 MKNK2 
                 AGXT2L2 
                 27 
               
               
                 Karpas422 
                 TRA2A 
                 IGF2BP3 
                 27 
               
               
                 Karpas422 
                 CDKL3andPPP2CA 
                 SKP1 
                 26 
               
               
                 KATOIII 
                 PAFAH1B2 
                 SIK3 
                 60 
               
               
                 KATOIII 
                 FGFR2 
                 ULK4 
                 18 
               
               
                 KATOIII 
                 FOXA2 
                 NCRNA00261 
                 7 
               
               
                 KATOIII 
                 UBA2 
                 WTIP 
                 6 
               
               
                 KATOIII 
                 CECR7andIL17RA 
                 LOC100132288 
                 3 
               
               
                 KATOIII 
                 NRIP1 
                 LOC100128341 
                 3 
               
               
                 KATOIII 
                 ZNF782 
                 ZNF510 
                 3 
               
               
                 KATOIII 
                 HDAC4 
                 ILKAP 
                 3 
               
               
                 KATOIII 
                 PLEKHM1P 
                 LOC146880 
                 3 
               
               
                 KATOIII 
                 CTNNB1 
                 ULK4 
                 3 
               
             
          
           
               
                 Table 3e Top ten highly-expressed fusion 
               
               
                 transcripts of LHCN-M2, LIM2405, LIM1899 and M059J. 
               
             
          
           
               
                 LHCN-M2 
                 ZNF782 
                 ZNF510 
                 91 
               
               
                 LHCN-M2 
                 EEF1DP3 
                 FRY 
                 69 
               
               
                 LHCN-M2 
                 TBC1D23 
                 NIT2 
                 30 
               
               
                 LHCN-M2 
                 MICAL3 
                 BCL2L13 
                 28 
               
               
                 LHCN-M2 
                 ADAM9 
                 ADAM32 
                 27 
               
               
                 LHCN-M2 
                 ZBED5 —   
                 KIAA0319L 
                 25 
               
               
                 LHCN-M2 
                 SLC7A5P2 
                 LOC641298 
                 25 
               
               
                 LHCN-M2 
                 NRIP1 
                 LOC100128341 
                 23 
               
               
                 LHCN-M2 
                 CTNNA1 
                 SIL1 
                 21 
               
               
                 LHCN-M2 
                 WLS 
                 DIRAS3 
                 19 
               
               
                 LIM2405 
                 VAX2 
                 ATP6V1B1 
                 5 
               
               
                 LIM2405 
                 SUMO2 
                 HN1 
                 3 
               
               
                 LIM2405 
                 ACCS 
                 EXT2 
                 3 
               
               
                 LIM2405 
                 CHCHD2 
                 PHKG1 
                 3 
               
               
                 LIM2405 
                 NRIP1 
                 LOC100128341 
                 2 
               
               
                 LIM2405 
                 XK 
                 CYBB 
                 2 
               
               
                 LIM2405 
                 ACCS 
                 EXT2 
                 2 
               
               
                 LIM2405 
                 SLC35A3 
                 HIAT1 
                 2 
               
               
                 LIM2405 
                 XK 
                 CYBB 
                 1 
               
               
                 LIM2405 
                 ZW10 
                 TMPRSS5 
                 1 
               
               
                 LIM1899 
                 UHRF1BP1L 
                 ANKS1B 
                 102 
               
               
                 LIM1899 
                 CDK13 
                 C7orf10 
                 14 
               
               
                 LIM1899 
                 MIR17HG 
                 GPC5 
                 12 
               
               
                 LIM1899 
                 ARNTL 
                 MICAL2 
                 9 
               
               
                 LIM1899 
                 UHRF1BP1L 
                 ANKS1B 
                 9 
               
               
                 LIM1899 
                 SLC35A3 
                 HIAT1 
                 8 
               
               
                 LIM1899 
                 LOC389641 
                 CHMP7 
                 7 
               
               
                 LIM1899 
                 ZNF619andZNF620 
                 ZNF621 
                 6 
               
               
                 LIM1899 
                 PLEKHM1P 
                 LOC146880 
                 5 
               
               
                 LIM1899 
                 UBA2 
                 WTIP 
                 5 
               
               
                 M059J 
                 SLC23A2 
                 RNF130 
                 51 
               
               
                 M059J 
                 NLGN1 
                 IFI6 
                 46 
               
               
                 M059J 
                 PRSS23 
                 PSMB2 
                 41 
               
               
                 M059J 
                 CPSF6 
                 ZNF532 
                 35 
               
               
                 M059J 
                 CYLD 
                 PHKB 
                 34 
               
               
                 M059J 
                 CCBL2 
                 MYO19 
                 33 
               
               
                 M059J 
                 KIAA1267 
                 ARL17AandARL17B 
                 31 
               
               
                 M059J 
                 HDAC8 
                 CITED1 
                 30 
               
               
                 M059J 
                 SIKE1andCSDE1andNRAS 
                 ZNF148andSLC12A8 
                 29 
               
               
                 M059J 
                 FLJ34690 
                 MYOCD 
                 26 
               
             
          
           
               
                 Table 3f Top ten highly-expressed fusion 
               
               
                 transcripts of MDA-MB-231, MG63, OCI-Ly7 and PC3 
               
             
          
           
               
                 MDA-MB-231 
                 SLC29A1 
                 HSP90AB1 
                 19 
               
               
                 MDA-MB-231 
                 REV1 
                 SUPT3H 
                 13 
               
               
                 MDA-MB-231 
                 HARS 
                 TTC27 
                 7 
               
               
                 MDA-MB-231 
                 SLC35A3 
                 HIAT1 
                 5 
               
               
                 MDA-MB-231 
                 LOC283299 
                 OVCH2 
                 4 
               
               
                 MDA-MB-231 
                 HARS 
                 TTC27 
                 4 
               
               
                 MDA-MB-231 
                 SLC35A3 
                 HIAT1 
                 4 
               
               
                 MDA-MB-231 
                 PDPK2 
                 TCEB2 
                 4 
               
               
                 MDA-MB-231 
                 TRIB3 
                 RBCK1 
                 3 
               
               
                 MDA-MB-231 
                 RPS6KB1 
                 TMEM49 
                 3 
               
               
                 MG63 
                 TFG 
                 GPR128 
                 495 
               
               
                 MG63 
                 DNER 
                 ELL2 
                 136 
               
               
                 MG63 
                 MTAPandCDKN2BAS 
                 BNC2 
                 121 
               
               
                 MG63 
                 THSD4 
                 LRRC49 
                 108 
               
               
                 MG63 
                 PSMD8 
                 ATF7andNPFF 
                 107 
               
               
                 MG63 
                 ELL2 
                 TRIP12 
                 78 
               
               
                 MG63 
                 HEATR7A 
                 PARP10 
                 76 
               
               
                 MG63 
                 TP53 
                 VAV1 
                 64 
               
               
                 MG63 
                 CLIP4 
                 EPHB4 
                 63 
               
               
                 MG63 
                 GAS6 
                 COMMD3andBMI1 
                 57 
               
               
                 OCI-Ly7 
                 IGL —   
                 GRAPL 
                 69 
               
               
                 OCI-Ly7 
                 PIK3C2 —   
                 UBE2D2 
                 41 
               
               
                 OCI-Ly7 
                 SIT1 
                 CD72 
                 38 
               
               
                 OCI-Ly7 
                 HIPK2 
                 NDUFA5 
                 38 
               
               
                 OCI-Ly7 
                 ZC3HAV1 
                 UBN2 
                 34 
               
               
                 OCI-Ly7 
                 LOC389641 
                 CHMP7 
                 33 
               
               
                 OCI-Ly7 
                 UBA2 
                 WTIP 
                 30 
               
               
                 OCI-Ly7 
                 AVL9 
                 SP4 
                 28 
               
               
                 OCI-Ly7 
                 PPFIA1 
                 RTN3 
                 27 
               
               
                 OCI-Ly7 
                 DNAJB1 
                 PKM2 
                 24 
               
               
                 PC3 
                 C12orf51 
                 RPL6 
                 53 
               
               
                 PC3 
                 SAMD8 
                 ADKandMRPL35P3 
                 41 
               
               
                 PC3 
                 PAAF1 
                 RPL141 
                 36 
               
               
                 PC3 
                 AGAP6 
                 FRMPD2 
                 29 
               
               
                 PC3 
                 ZMIZ1 
                 CTNNA3 
                 26 
               
               
                 PC3 
                 FAF1 
                 AGBL4 
                 25 
               
               
                 PC3 
                 MPP5 
                 FUT8 
                 25 
               
               
                 PC3 
                 C1orf55 
                 ENAH 
                 25 
               
               
                 PC3 
                 MAD1L1 
                 CHFRandGOLGA3 
                 24 
               
               
                 PC3 
                 PTK2 
                 SKP1 
                 24 
               
             
          
           
               
                 Table 3g Top ten highly-expressed fusion 
               
               
                 transcripts of RPMI-7951, SJCRH30, SK-Mel-5 and SK-N-DZ 
               
             
          
           
               
                 RPMI-7951 
                 RPS5P1andDSE 
                 FAM26F 
                 26 
               
               
                 RPMI-7951 
                 RPS11andSNORD35B 
                 LUC7L 
                 23 
               
               
                 RPMI-7951 
                 MYO19 
                 ZNHIT3 
                 22 
               
               
                 RPMI-7951 
                 LHFP 
                 CREBZF 
                 22 
               
               
                 RPMI-7951 
                 EEF1DP3 
                 FRY 
                 22 
               
               
                 RPMI-7951 
                 ZNF649andZNF577 
                 TATDN2andGHRLOS 
                 22 
               
               
                 RPMI-7951 
                 UTRN 
                 NME7 
                 20 
               
               
                 RPMI-7951 
                 TRIO 
                 CYBRD1 
                 19 
               
               
                 RPMI-7951 
                 CRTC3 
                 MAPKBP1 
                 19 
               
               
                 RPMI-7951 
                 TOPORSandDDX58 
                 ACO1 
                 19 
               
               
                 SJCRH30 
                 MARS 
                 AVIL 
                 714 
               
               
                 SJCRH30 
                 PAX3 
                 FOXO1 
                 283 
               
               
                 SJCRH30 
                 SNORD114-1 
                 MEG8- 
                 135 
               
               
                 SJCRH30 
                 MEGF11 
                 RPL9P25andTIPIN 
                 44 
               
               
                 SJCRH30 
                 RPS6KC1 
                 FLVCR1 
                 40 
               
               
                 SJCRH30 
                 FANCD2 
                 MTHFD1L 
                 32 
               
               
                 SJCRH30 
                 THSD4 
                 SERHL2 
                 27 
               
               
                 SJCRH30 
                 ZNF782 
                 ZNF510 
                 26 
               
               
                 SJCRH30 
                 NRIP1 
                 LOC100128341 
                 23 
               
               
                 SJCRH30 
                 RAD18 
                 OXTR 
                 23 
               
               
                 SK-Mel-5 
                 C1orf43 
                 SCAMP3 
                 1067 
               
               
                 SK-Mel-5 
                 UBE2Q1 
                 VPS72andTMOD4 
                 279 
               
               
                 SK-Mel-5 
                 FSTL5 
                 MRPL21 
                 65 
               
               
                 SK-Mel-5 
                 LOC340357 
                 LONRF1 
                 27 
               
               
                 SK-Mel-5 
                 ZNF782 
                 ZNF510 
                 27 
               
               
                 SK-Mel-5 
                 C1orf43 
                 SCAMP3 
                 21 
               
               
                 SK-Mel-5 
                 CTTN 
                 TRIM37 
                 20 
               
               
                 SK-Mel-5 
                 DIXDC1 
                 SDHD 
                 17 
               
               
                 SK-Mel-5 
                 TUFT1 
                 EFNA4andEFNA3 
                 17 
               
               
                 SK-Mel-5 
                 LOC729082 
                 RGS20 
                 17 
               
               
                 SK-N-DZ 
                 MAP1D 
                 FARSB 
                 1327 
               
               
                 SK-N-DZ 
                 KIAA1267 
                 ARL17AandARL17B 
                 682 
               
               
                 SK-N-DZ 
                 CTSC 
                 MAML2 
                 134 
               
               
                 SK-N-DZ 
                 DBI 
                 SPAG16 
                 66 
               
               
                 SK-N-DZ 
                 AACSL 
                 ZNF354A 
                 57 
               
               
                 SK-N-DZ 
                 C2orf43 
                 FLJ30838 
                 57 
               
               
                 SK-N-DZ 
                 KLK4 
                 KLKP1 
                 55 
               
               
                 SK-N-DZ 
                 PSMB7 
                 CKS2 
                 55 
               
               
                 SK-N-DZ 
                 CAPZA2 
                 PTTG1 
                 54 
               
               
                 SK-N-DZ 
                 SNORD114-1 
                 MEG8 
                 53 
               
             
          
           
               
                 Table 3h Top ten highly-expressed fusion 
               
               
                 transcripts of SK-N-SH, SUN-16, Hela-3 and REC1. 
               
             
          
           
               
                 SK-N-SH 
                 EXOC4 
                 PVT1 
                 235 
               
               
                 SK-N-SH 
                 C19orf47 
                 AKT2 
                 225 
               
               
                 SK-N-SH 
                 EXOC4 
                 PVT1 
                 142 
               
               
                 SK-N-SH 
                 PAOXandMTG1 
                 LOC619207 
                 131 
               
               
                 SK-N-SH 
                 ACCS 
                 EXT2 
                 116 
               
               
                 SK-N-SH 
                 VAX2 
                 ATP6V1B1 
                 111 
               
               
                 SK-N-SH 
                 PVT1 
                 EXOC4 
                 107 
               
               
                 SK-N-SH 
                 LMAN2 
                 MXD3andRAB24 
                 93 
               
               
                 SK-N-SH 
                 MFGE8 
                 HAPLN3 
                 87 
               
               
                 SK-N-SH 
                 RPL23AP5 
                 NME4andDECR2 
                 84 
               
               
                 SUN16 
                 PVT1 
                 SLC1A2 
                 22 
               
               
                 SUN16 
                 PVT1 
                 SLC1A2 
                 14 
               
               
                 SUN16 
                 LOC389641 
                 CHMP7 
                 4 
               
               
                 SUN16 
                 STS 
                 VCX 
                 4 
               
               
                 SUN16 
                 EEF1DP3 
                 FRY 
                 4 
               
               
                 SUN16 
                 CTNNBIP1 
                 CLSTN1 
                 4 
               
               
                 SUN16 
                 CENPK 
                 UVRAG 
                 4 
               
               
                 SUN16 
                 NDUFAF2 
                 ZSWIM6 
                 4 
               
               
                 SUN16 
                 RND3 
                 RALB 
                 4 
               
               
                 SUN16 
                 CMIP 
                 DYNLRB2 
                 4 
               
               
                 Hela-3 
                 RPS6KB1 
                 TMEM49 
                 256 
               
               
                 Hela-3 
                 HNRNPUL2andBSCL2 
                 C11orf49 
                 253 
               
               
                 Hela-3 
                 GNB1 
                 NADK 
                 149 
               
               
                 Hela-3 
                 ST6GALNAC4 
                 ST6GALNAC6andAK1 
                 124 
               
               
                 Hela-3 
                 KIAA1267 
                 ARL17AandARL17B 
                 120 
               
               
                 Hela-3 
                 CCDC123 
                 PEPD 
                 79 
               
               
                 Hela-3 
                 UBA2 
                 WTIP 
                 64 
               
               
                 Hela-3 
                 PAOXandMTG1 
                 LOC619207 
                 49 
               
               
                 Hela-3 
                 GNB1 
                 NADK 
                 47 
               
               
                 Hela-3 
                 C19orf47 
                 AKT2 
                 42 
               
               
                 REC1 
                 AKNA 
                 FBXL20 
                 98 
               
               
                 REC1 
                 FBXL20 
                 AKNA 
                 41 
               
               
                 REC1 
                 MYST3 
                 PLEKHA5 
                 27 
               
               
                 REC1 
                 LOC619207 
                 CYP2E1 
                 20 
               
               
                 REC1 
                 FCRL2 
                 FCRL3 
                 18 
               
               
                 REC1 
                 SLC29A1 
                 HSP90AB1 
                 18 
               
               
                 REC1 
                 ZNF782 
                 ZNF510 
                 14 
               
               
                 REC1 
                 LOC285972 
                 GIMAP8 
                 13 
               
               
                 REC1 
                 PAOXandMTG1 
                 LOC619207 
                 12 
               
               
                 REC1 
                 ST6GALNAC4 
                 ST6GALNAC6andAK1 
                 11 
               
             
          
           
               
                 Table 3i Top ten highly-expressed fusion 
               
               
                 transcripts of U87, U2OS, U251 and MCF7. 
               
             
          
           
               
                 U87 
                 BMP7 
                 TMPRSS15 
                 10 
               
               
                 U87 
                 PPP1R13L 
                 ZNF541 
                 9 
               
               
                 U87 
                 PPP1R13L 
                 ZNF541 
                 5 
               
               
                 U87 
                 ZNF782 
                 ZNF510 
                 5 
               
               
                 U87 
                 CDKL3andPPP2CA 
                 SKP1 
                 5 
               
               
                 U87 
                 BMP7 
                 TMPRSS15 
                 4 
               
               
                 U87 
                 UBA2 
                 WTIP 
                 3 
               
               
                 U87 
                 SACS 
                 SGCG 
                 3 
               
               
                 U87 
                 C15orf26 
                 IL16 
                 2 
               
               
                 U87 
                 ATP2C1 
                 NEK11 
                 2 
               
               
                 U2OS 
                 ADAM9 
                 ADAM32 
                 33 
               
               
                 U2OS 
                 UBA2 
                 WTIP 
                 6 
               
               
                 U2OS 
                 SLC35A3 
                 HIAT1 
                 4 
               
               
                 U2OS 
                 MRPS10 
                 GUCA1B 
                 3 
               
               
                 U2OS 
                 HDAC8 
                 CITED1 
                 3 
               
               
                 U2OS 
                 BAG4 
                 DDHD2 
                 2 
               
               
                 U2OS 
                 BAG4 
                 DDHD2 
                 1 
               
               
                 U251 
                 ATP11C 
                 MCF2 
                 49 
               
               
                 U251 
                 NRIP1 
                 LOC100128341 
                 6 
               
               
                 U251 
                 RASSF8 
                 SSPN 
                 4 
               
               
                 U251 
                 RAB31 
                 TXNDC2 
                 4 
               
               
                 U251 
                 LARP1 
                 CNOT8 
                 4 
               
               
                 U251 
                 ARF3 
                 FKBP11 
                 3 
               
               
                 U251 
                 CORO1C 
                 SELPLG 
                 3 
               
               
                 U251 
                 PPP1R12A 
                 PAWR 
                 3 
               
               
                 MCF7 
                 ARFGEF2 
                 SULF2 
                 2176 
               
               
                 MCF7 
                 RPS6KB1 
                 TMEM49 
                 2107 
               
               
                 MCF7 
                 TANC2 
                 CA4 
                 1526 
               
               
                 MCF7 
                 RPS6KB1 
                 TMEM49 
                 1502 
               
               
                 MCF7 
                 PAPOLA 
                 AK7 
                 873 
               
               
                 MCF7 
                 SYTL2 
                 PICALM 
                 764 
               
               
                 MCF7 
                 ADAMTS19 
                 SLC27A6 
                 685 
               
               
                 MCF7 
                 RPS6KB1 
                 DIAPH3 
                 597 
               
               
                 MCF7 
                 ABCA5 
                 PPP4R1L 
                 535 
               
               
                 MCF7 
                 DEPDC1B 
                 ELOVL7 
                 532 
               
             
          
           
               
                 Table 3j Top ten highly-expressed fusion 
               
               
                 transcripts of HepG2, K562 and SJSA1. 
               
             
          
           
               
                 HepG2 
                 AHSG 
                 GYG2P1andARSFP1 
                 308 
               
               
                 HepG2 
                 FOXA2 
                 NCRNA00261 
                 252 
               
               
                 HepG2 
                 ZNF782 
                 ZNF510 
                 142 
               
               
                 HepG2 
                 LMO7 
                 UCHL3 
                 134 
               
               
                 HepG2 
                 LMAN2 
                 MXD3andRAB24 
                 90 
               
               
                 HepG2 
                 NRIP1 
                 LOC100128341 
                 78 
               
               
                 HepG2 
                 PAOXandMTG1 
                 LOC619207 
                 71 
               
               
                 HepG2 
                 VAX2 
                 ATP6V1B1 
                 70 
               
               
                 HepG2 
                 SLC29A1 
                 HSP90AB1 
                 58 
               
               
                 HepG2 
                 NRIP1 
                 LOC100128341 
                 58 
               
               
                 K562 
                 BCR 
                 ABL1 
                 4043 
               
               
                 K562 
                 BAT3 
                 SLC44A4 
                 2760 
               
               
                 K562 
                 NUP214 
                 XKR3 
                 2443 
               
               
                 K562 
                 KIAA1267 
                 ARL17AandARL17B 
                 781 
               
               
                 K562 
                 C10orf76 
                 KCNIP2andMGEA5 
                 432 
               
               
                 K562 
                 IMMP2L 
                 DOCK4 
                 254 
               
               
                 K562 
                 C15orf26 
                 IL16 
                 218 
               
               
                 K562 
                 C16orf87 
                 ORC6L 
                 202 
               
               
                 K562 
                 PRIM1 
                 NACA 
                 188 
               
               
                 K562 
                 BAT3 
                 SLC44A4 
                 171 
               
               
                 SJSA1 
                 HMGA2 
                 LUM 
                 4210 
               
               
                 SJSA1 
                 ARHGEF7 
                 CPM 
                 281 
               
               
                 SJSA1 
                 SNORD114-1 
                 MEG8 
                 113 
               
               
                 SJSA1 
                 SLC7A5 
                 BANP 
                 107 
               
               
                 SJSA1 
                 SP140L 
                 LCA5 
                 96 
               
               
                 SJSA1 
                 KIF5A 
                 STK24 
                 94 
               
               
                 SJSA1 
                 KPNA6 
                 UBAP2L 
                 69 
               
               
                 SJSA1 
                 KIAA0427 
                 SMAD2 
                 57 
               
               
                 SJSA1 
                 AGRN 
                 TMEM8A 
                 51 
               
               
                 SJSA1 
                 SLC12A2 
                 DDX5 
                 51 
               
               
                   
               
             
          
         
       
     
         [0094]    To characterize these large numbers of fusion transcripts, we have analyzed the fusion transcripts based on cancer cell lines and their supporting sequence reads. Table 3 has shown that many fusion transcripts are expressed at very high levels. However, they are often detected only in one type of cancer and are not recurrent in other cancer types. One of the most highly-expressed putative fusion genes is HMGA2-LUM putative fusion gene in osteosarcoma SJSA1 cell, which is a putative fusion gene between HMGA2 gene, encoding high mobility group AT-hook2 and associated with mesenchymoma and LUM gene coding for lumican and associated with corneal dystrophy.  FIG. 7 a    shows that HMGA2 and LUM genes have undergone potential intra-chromosomal translocations and they are brought to close each other on the chromosome 12.  FIG. 7 b    shows that HMGA2-LUM fusion gene has two isoforms (Isoform 1 and Isoform 2).  FIG. 7 b    shows that Isoform 1 and Isoform 2 differ by only two nucleotides at their fusion junctions. Isoform 1 will have the normal LUM&#39;s last exon and generate a HMGA2-LUM fusion protein. On the hand, Isoform 2 will result in a truncated HMGA2 protein, which is 50 amino acids shorter than the Isoform 1.  FIG. 7 c    shows that two expression levels differ by 4200 folds. The fact that HMGA2 isoforms similar to Isoform 2 have been observed in normal human tissues and cells has suggested that the Isoform 1 fusion protein may play in important role in SJSA1 cancer development. 
         [0095]    As discussed above, we have adopted much stringent conditions to identify fusion transcripts. As shown in Table 2, our supporting sequence reads are 7.5 folds less than others. Technically, it is much more difficult for us to experimentally verify the lowly-expressed fusion transcripts than those highly-expressed fusion transcripts. Since we have identified large numbers of fusion transcripts, it is not practical for us to use “traditional” RT-PCR approaches and other “traditional” methods to validate these large numbers of fusion transcripts. However, if we can use the traditional RT-PCR methods to validate some lowly-expressed fusion transcripts, it will greatly help us to understand the characteristics of these fusion transcripts and will lay solid foundations for large-scale verification of all fusion transcripts, such as RNA CaptureS eq (Mercer, et al. 2014). 
         [0096]    To verify the lowly-expressed fusion transcripts, we have isolated total RNAs from cancer cell lines MCF-7, Hela-3, HepG2, BT-474, K562, 293T and other cancer cell lines while GM12878 and MCF-10A normal cell line have been used as controls. Total RNAs are isolated by Qiagen RNeasy mini columns with DNase I digestion as suggested by the manufacturer. Briefly, 1×10 6  cultured cells are harvested by centrifuging for 5 min at 300×g. Supernatants are removed by aspiration. Cell pellets are disrupted for 30 seconds in 350 μl of Buffer RLT. The lysates are pipetted directly into a QIAshredder spin column placed in a 2 ml collection tube, and centrifuge for 2 min at full speed. One volume of 70% ethanol is added to the cleared lysate, and mix well by pipetting. 700 μl of the sample are transferred to RNeasy mini spin columns sitting in a 2-ml collection tube and the columns are centrifuged for 30 seconds at maximum speed and flow-through is discarded. 700 μl Buffer RW1 are added onto the RNeasy column, the RNeasy columns are centrifuged for 30 seconds at maximum speed and flow-through is discarded. 350 μl Buffer RWT are added into the RNeasy Mini spin column and centrifuge for 15 at 8000×g. To remove potential DNA contamination, after 10 μl DNase I stock solution is mixed with 70 μl Buffer RDD by gently inverting tubes, the DNase solution is added into the RNeasy columns and incubated at room temperature for 30 minutes. The columns are washed again by adding 350 μl Buffer RWT. After RNeasy columns are transferred to new 2-ml collection tubes, the columns are washed twice using 500 μl Buffer RPE by centrifuging for 30 seconds at maximum speed. RNAs are eluted from the columns by adding 30 μl of RNase-free water 
         [0097]    The first-strand cDNA synthesis is carried out using oligo(T)15 and/or random hexamers by TaqMan Reverse Transcription Reagents (Applied Biosystems Inc., Foster City, Calif., USA) as suggested by the manufacturer. In brief, to prepare the 2×RT master mix, we pool 10 μl of reaction mixes containing final concentrations of 1×RT Buffer, 1.75 mM MgCl 2 , 2 mM dNTP mix (0.5 mM each), 5 mM DTT, 1× random primers, 1.0 U/μl RNase inhibitor and 5.0 U/μl MultiScribe®. The master mixes are prepared, spanned down and placed on ice. 10 μl of 2×RNA mixes containing 2 ug of total RNA are added into 10 μl 2× master mixes and mixed well. The reaction mixes are then placed in a thermal cycler of 25° C., 10 min, 37° C. 120 min, 95° C., 5 min and 4° C., ∞. The resulted cDNAs are diluted by 80 μl of H 2 O. 
         [0098]    To identify novel human fusion transcripts, fusion transcript specific primers have been designed to cover the 5′ and 3′ fusion transcripts. The primers are designed using the primer-designing software (SDG 2015). 5 μl of the cDNAs generated above are used to amplify fusion transcripts by PCR. PCR amplifications are carried out by HiFi Taq polymerase (Invitrogen, Carlsbad, Calif., USA). PCR reactions have been carried out by HiFi Taq polymerase (Invitrogen, Carlsbad, Calif., USA) using cycles of 94° C., 15″, 60-68° C., 15″ and 68° C., 2-5 min. The PCR products are separated on 2% agarose gels. The expected products are excised from gels and cloned into pCR4.0 TA vector (Invitrogen, Carlsbad, Calif., USA). Fusion transcripts are then verified by blast and manual inspection. 
         [0099]    As discussed above, many highly-expressed fusion transcripts have been successfully validated in different cancer datasets. In our approach, we have identified majorities of fusion transcripts are expressed at very low levels based on the numbers of supporting sequence reads. After we have performed RNA-seq analysis of different lymphoblastoid cell lines from different individuals, we have found that lowly-expressed fusion transcripts are shown to have strong individuality. That is, these fusion transcripts can be detected only in one lymphoblastoid cell line, but not in any of other lymphoblastoid cell lines. Later, experimental data have confirmed this conclusion. So we have selected numbers of lowly-expressed fusion transcripts for validation and we have validated six of them so far. 
         [0100]    Table 4 shows the list of the validated fusion transcripts expressed at very 
         [0000]                                                        TABLE 4                   Characteristics of some lowly-expressed fusion transcripts       validated by RT-PCR and following by DNA sequencing.                Fusion Transcripts   Cell Types   NSJMR                            GABBR1andUBD|PSPH   BT-474   0.001           ncRNA00188_|GNAI3   GM12878   0.00051           LRRC37A3|VNN2   BT-474   0.000891           CPSF6|CACNA1E   GM12878   0.000455           FAM164A|RASA4PandPOLR2J4   Heart   0.000394           RRP8|RAB2A   Heart   0.00095                        
low levels, which range from 3.94×10 −4  to 1×10 −3  numbers of splice junctions per million reads (NSJMR).
 
         [0101]    Table 5 shows the primers used to validate the fusion transcripts. 
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 5 
               
             
             
               
                   
               
               
                 List of primers for validation of fusion transcripts. 
               
             
          
           
               
                 Fusion Transcripts 
                 5′ Primers 
                 3′ Primers 
               
               
                   
               
               
                 GABBR1andUBD|PSPH 
                 TGAGTAGCTGAAACTACAGGATGCTT 
                 TCAGTGATATACCATTTGGCGTT, 
               
               
                   
               
               
                 ncRNA00188_|GNAI3 
                 CACAGTGGGGGTGTGCAAAC 
                 CGAGACCGTGACCGAGAG 
               
               
                   
               
               
                 LRRC37A3|VNN2 
                 TGAGTAGCTGGGATTGCAGTACCA 
                 TCCGGCTTTTCAGGGACATTAA 
               
               
                   
               
               
                 CPSF6|CACNA1E 
                 CGAGACCGTGACCGAGAG 
                 CGAGACCGTGACCGAGAG 
               
               
                   
               
               
                 FAM164A|RASA4PandPOLR2I4 
                 CCTCCCCAACCAAGCTTTCTGTA 
                 CCTTCAATGCCTTTAATATTTCCACC 
               
               
                   
               
               
                 RRP8|RAB2A 
                 GATGTTCGAACCTTTCTGCGG 
                 ACGACCTTGTGATGGAACGAAA 
               
               
                   
               
             
          
         
       
     
         [0102]    As shown in Table 4, the CPSF6|CACNA1E fusion transcripts have been found to be expressed at very low levels in the lymphoblastoid cell line of GM12878 and its NSJMR is 4.55×10 −10 . CPSF6 gene, encoding Cleavage And Polyadenylation Specific Factor 6, has been shown to be located on the chromosome 12 while CACNA1E gene, coding for Calcium Channel, R Type, Alpha-1 Polypeptide, is locate on the chromosome 1. The CPSF6|CACNA1E fusion transcripts are interchromosomal translocations.  FIG. 8  has shown a schematic diagram of procedures to verify CPSF6|CACNA1E fusion transcripts in lymphoblastoid cell line. A potential translocation has brought CPSF6 and CACNA1E genes together. Total RNAs are isolated from the GM12878 cell lines and cDNAs are generated by TaqMan Reverse Transcription Reagents. Pair of primers has been designed to amplify cDNAs. The amplified DNAs are separated on a 2.0% agarose gel. The DNA fragments are isolated by QIAquick Gel Extraction Kit and are cloned into pCR4.0 TA vector (Invitrogen, Carlsbad, Calif., USA). The plasmid DNAs of the positive clones are isolated and sequenced. The sequenced data are used by blast and manual inspection to verify the fusion junctions ( FIG. 8 ). The CPSF6|CACNA1E fusion transcript suggests that the in-frame CPSF6|CACNA1E fusion gene has eight exons of the CPSF6 nine exons and forty-eight exons of the CACNA1E forty-nine exons, which are much larger than both proteins. 
         [0103]    In addition, we have verified two fusion transcripts, RRP8|RAB2A and FAM164A|RASA4PandPOLR2J4 in heart tissues from patients with heart diseases. As we have observed above, the fusion transcripts have been shown to have individuality. The validation of these lowly-expressed fusion transcripts have suggested that the many of the lowly-expressed fusion transcripts may play important roles in cancer initiation, developments, invasion, and metastasis. 
         [0104]    To check whether these three fusion transcripts are expressed in other cancer cell lines, we have used identical conditions to perform individual RT-PCR amplification of cDNAs from these cancer cell lines described above without success. We have tested different experimental conditions without any success. Since we have such large numbers of lowly-expressed fusion transcripts, we need more efficient method to validate these fusion transcripts in varieties of tissues, cells and individuals. 
         [0105]    Table 3 shows that many top fusion transcripts are from read-though and recurrent in many cell lines.  FIG. 9 a    shows MTG1 and SCART1 (LOC609217) on the chromosome 10, which encodes mitochondrial GTPase 1 homolog and a pseudogene of scavenger receptor protein family member, respectively. The read-though has resulted in fusion transcripts between MTG1 and SCART1 genes. Eight isoforms have been identified. Five fusion transcripts are 5′ alternatively-spliced at the MTG1 exon 10 while the remaining 3 fusion transcripts are alternatively-spliced at the MTG1 exon 11. These data have clearly shown that MTG1|SCART1 fusion gene is alternatively spliced and are able to generate in-frame hybrid proteins ( FIG. 9 b   ). These data have demonstrated that read-though fusion genes are similar to normal genes. MTG1|SCART1 isoform 1 has been the dominant isoform ( FIG. 8 c   ) and could generate a fusion protein containing majority of MTG1 and major part of SCART1 protein.  FIG. 9 d    has shown that MTG1|SCART1 fusion transcripts have been detected in 29 out of 39 cancer cell lines.  FIG. 9 e    shows that the expression levels among different types of cancer are significantly different and the ratios of different isoforms also differed significantly. 
         [0106]    Read-through fusion transcripts are significantly different from the other four fusion transcripts. That is, two parental genes of fusion transcripts are close each other on the same chromosomes with the same orientations. Even though some read-though fusion transcripts may be caused by genetic alternations, majorities of read-though fusion transcripts may be due to failures of fail-safe transcriptional mechanisms (Porrua and Libri 2015). Many aberrant environmental and developmental factors often result in failures of transcriptional terminations and generate read-though fusion transcripts. More importantly, majority of fusion transcripts may be tissues-specifically expressed and have special functions. To verify whether expression of read-through fusion transcripts is tissues-specific, we have performed analysis of RNA-seq datasets of normal human tissues which include tissue samples from 95 human individuals representing 27 different tissues and primary cell lines (ENCODE 2015, SCILIFELAB 2015). Read-though fusion transcripts from different tissues have been used as negative controls to analyze cancer fusion transcripts. 
         [0107]      FIG. 10 a    shows an example demonstrating differential expression patterns of read-through fusion transcripts in normal tissues. The C19orf47 and AKT2 genes are located the chromosome 19 and are separated by 57 Kb.  FIG. 10 a    has shown that the C19orf47|ATK2 fusion transcripts have been detected in bone marrow, colon, duodenum, Fallopian tube, fat gall bladder, testis, thyroid, tonsil but they are not found in other 18 other tissues as well as breast tissues and HMEC. In addition,  FIG. 10 a    has also demonstrated that C19orf47|AKT2 fusion transcripts are expressed at significantly different levels among these nine tissues. 
         [0108]    To demonstrate how to use read-though fusion transcripts as cancer biomarkers, we have performed analysis of breast cancer data from HudsonAlpha Institute for Biotechnology, AL, USA (designed as HIBCD) (Varley, et al. 2014), which have 168 breast cancer samples.  FIG. 10 b    has shown that 7 (4%) breast cancer samples have been shown to express C19orf471ATK2 fusion transcripts out of the HIBCD 168 breast cancer samples. 
         [0109]    To further demonstrate how to use read-though fusion transcripts as cancer biomarkers, we have performed analysis of both HIBCD and South Korean breast cancer data (designed as SKBCP) (ERP010142 2015). Then we have performed comparative analyses of the fusion transcripts from normal human tissues and the HIBCD breast cancer samples.  FIG. 11  has shown that GAL3ST2 gene, encoding galactose-3-O-sulfotransferase 3, and NEU4 gene, coding for N-Acetyl-Alpha-Neuraminidase 4, are located on the chromosome 11 and are separated by 17 Kb. GAL3ST2 gene has been implicated in tumor metastasis processes while NEU4 gene has been associated with NEU4 include galactosialidosis. The GAL3ST2|NEU4 fusion transcripts are expressed only in normal human colon and absent in 26 other human tissues, breast and human mammary epithelial cells (HMEC). As shown in  FIG. 11 , we have detected GAL3ST2|NEU4 fusion transcripts in 5 (3%) samples out of the 168 HIBCD breast cancer samples, two of which have much significantly higher expression levels than that in colon tissues. On the other hand, we have detected GAL3ST2|NEU4 fusion transcripts in only one (1.3%) sample out of 78 SKBCP breast cancer patients. These data have suggested that GAL3ST2|NEU4 fusion transcripts are far less frequent than what people have expected. This has demonstrated that read-though fusion transcripts can be used to test whether they are expressed in wrong tissues and wrong developmental stages. 
         [0110]    As shown in  FIG. 4 d   , in addition to read-through, inversions have much more recurrent fusion transcripts than those of interchromosomal translocations, intrachromosomal translocations and deletions. So we have examined inversion fusion transcripts and identified large numbers of recurrent fusion transcripts as potential cancer detection biomarkers. Table 3 has shown that many high-expressed fusion transcripts come from inversions or duplications. One of the highly-expressed fusion transcripts is KANSL1 (KIAA1267)|ARL17A reported previously (Kinsella, et al. 2011), which is resulted from a chromosome 17 inversion ( FIG. 12 a   ).  FIG. 12 b    has shown that the KANSL1|ARL17A fusion gene generates six fusion transcripts, which can produce potential KANSL1|ARL17A fusion proteins, five of which are novel fusion transcripts.  FIG. 9 c    has shown that fusion transcript 2 is expressed at the highest levels among the six fusion transcripts.  FIG. 12 d    has shown that the KANSL1|ARL17A fusion transcripts have been found in 14 out of 39 cancer cell lines and the largest and the second largest numbers of KANSL1|ARL17A fusion transcripts have been found in K562 and SK-N-DZ cancer cell lines. To rule out the size effects of RNA-seq datasets, we have normalized expression of the KANSL1|ARL17A fusion transcripts.  FIG. 12 e    has shown that the highest expressed fusion transcripts have been found in Karapas-422 cancer cell line. A549, H4, HT29, A375, SK-N-SH, and K562 are among highly-expressed cancer cell lines ( FIG. 12 e   ). KANSL1 gene, located in 17q21.31, encodes KAT8 regulatory NSL complex subunit involved with histone acetylation and is associated with koolen de vries syndrome, formerly known as 17q21.31 microdeletion syndrome (Koolen, et al. 2006, de Jong, et al. 2012). Chromosomal band 17q21.31 contains common recurrent inversions in 20% population with European ancestry (Stefansson, et al. 2005). Based on the information of cancer cell lines, the majorities of the ECD39 cancer cell lines are Caucasian, which suggests their European ancestry. Our KANSL1|ARL17A fusion transcript data and genetic data (Koolen, et al. 2006, de Jong, et al. 2012) have suggested that KANSL1|ARL17A fusion transcripts are associated with recurrent inversions of the chromosomal band 17q21.31. 
         [0111]    To explore whether the fusion transcripts can be used to investigate relationships between human evolutionary genetics and fusion transcripts, we have plotted the total fusion transcripts and inversion fusion transcripts along the human chromosome 17.  FIG. 13 a    shows the relationships between the total fusion transcripts and inversion fusion transcripts and chromosome positions, each of which represents 5M bp.  FIG. 13 a    shows that there is peaks of both total and inversion fusion transcripts between 41 Mb and 49 Mb. When we have plotted total fusion transcripts identified in ≧2 cancer cell lines and inversion fusion transcripts detected in ≧2 cancer cell lines along the human chromosome 17,  FIG. 13 b    has shown patterns similar to those in  FIG. 13 a    and locations of KANSL1|ARL17A fusion transcripts are indicated by arrows. These suggest that the region from 41 Mb to 49 Mb of the chromosome 17q21.31 band is associated with numbers of other recurrent fusion transcripts. In addition, we have found that three additional peaks may be associated with human genetic variations on the chromosome 17. 
         [0112]    As we discussed above, we can use the hit maps of fusion transcripts to discover and locate recurrent chromosomal regions associated with cancers. We have plotted the hit maps of total fusion transcripts and inversion fusion transcripts.  FIG. 14  shows the genome-wide hit maps of the total fusion transcripts detected in ≧2 cancer cell lines and inversion fusion transcripts detected in ≧2 cancer cell lines. The peaks in each hit map represent variable regions and may be associated with cancer. 
         [0113]      FIG. 13 a    and  FIG. 13 b    have shown that chromosomal band 17q21.31 contains multiple fusion transcripts. Table 6 shows 18 putative fusion genes from 41 Mb to 49 Mb of the chromosome 17q21.31 region, which are pointed by arrows and are supported by 34 fusion transcripts. Clustering large numbers of fusion transcripts suggests that certain genetic variations make these regions unstable and often result in genetic alternations, which generate fusion transcripts. 
         [0000]    
       
         
               
             
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 6 
               
             
             
               
                   
               
               
                 List of fusion transcripts detected between 42 Mb to 48 Mb of 
               
               
                 the chromosome 17. 
               
             
          
           
               
                 5′ Gene 
                 5′ Positions (Mb) 
                 3′ Gene 
                 3′ Positions (Mb) 
               
               
                   
               
             
          
           
               
                 LRRC37A4 
                 43.6 
                 NSF 
                 44.7 
               
               
                 LRRC37A4 
                 43.7 
                 NMT1 
                 43.2 
               
               
                 LRRC37A4 
                 43.7 
                 KIAA1267 
                 44.2 
               
               
                 LRRC37A4 
                 43.7 
                 LRRC37A3 
                 62.9 
               
               
                 LRRC37A4 
                 43.7 
                 ARSG —   
                 66.3 
               
               
                 C17orf69 
                 43.7 
                 ARHGAP27 
                 43.5 
               
               
                 KIAA1267 
                 44.1 
                 ARL17A 
                 44.6 
               
               
                 ARL17A 
                 44.6 
                 KIAA1267 
                 44.2 
               
               
                 NSF 
                 44.8 
                 LRRC37A3 
                 62.9 
               
               
                 MRPL45P2 
                 45.5 
                 NPEPPS 
                 45.6 
               
               
                 NPEPPS 
                 45.7 
                 ITGB3 —   
                 45.5 
               
               
                 MRPL10 
                 45.9 
                 KIAA0100 —   
                 27 
               
               
                 HOXB6 
                 46.7 
                 BAIAP2 
                 79 
               
               
                 ATP5G1 
                 47 
                 UBE2Z 
                 47 
               
               
                 GIP 
                 47 
                 SNF8 
                 47 
               
               
                 SPOP 
                 47.7 
                 NME1-NME2 
                 49.2 
               
               
                   
               
             
          
         
       
     
         [0114]    It has been reported that the H2 lineage is rare in Africans, almost absent in East Asians, but found in 20% population with European ancestry (Stefansson, et al. 2005). To further confirm the inversion KANSL1|ARL17A fusion transcript is a cancer-biomarker associated with European genetic backgrounds, we have performed analysis of HIBCD and SKBCP breast cancer data (Varley, et al. 2014, ERP010142 2015). The HIBCD contains 168 breast cancer cell lines and primary breast cancer tissues samples (Varley, et al.). The SKBCP has samples from 22 HRM (high-risk for distant metastasis) and 56 LRM (low-risk for distant metastasis) breast cancer patients (ERP010142 2015). We have performed comparative analyses of HIBCD and SKBCP samples.  FIG. 15  has shown that HIBCD has 50 samples that express KANSL1|ARL17A fusion transcripts while the SKBCP has none of the KANSL1|ARL17A samples. The difference between HIBCD and SKBCP has been shown by χ 2 -test to be statistically significant (p≧0.001). SKBCP has 100 bp RNA-seq reads and has total 1.6×10 12  base counts while HIBCD has 50 bp RNA-seq reads in length and has total 1.2×10 12  base counts. Therefore, the qualities of the SKBCP dataset are better than those of the HIBCD. These data have ruled out that the KANSL1|ARL17A fusion transcripts are caused by experimental errors and random chances. The absence of the SKBCP KANSL1|ARL17A samples not only has further confirmed that any fusion transcript identified by our splicingcodes method are not generated by random chance or experimental errors, but also have shown that KANSL1|ARL17A fusion transcripts are associated with breast cancer patients of European ancestry. 
         [0115]    Since the KANSL1|ARL17A fusion proteins are involved with histone acetylation and may affect the chromosomal stabilities, it is highly unlikely that they directly cause cancer in a short time and may be earlier cancer biomarkers (de Jong, et al. 2012). However, their expression will have tremendous affects on the cancer initiation, developments, invasion, and metastasis. In order to understand their expression, we have analyzed expression levels in the HIBCD 50 cancer samples.  FIG. 16  has shown that the KANSL1|ARL17A expression levels of HIBCD 50 samples are significantly different and range from 0.0113 to 0.18 NSJMR. The lowest and highest expression levels differ by 16 folds.  FIG. 16  has also shown that the KANSL1|ARL17A fusion transcripts are not detected in the normal breast tissues and HMEC even though their RNA-seq datasets are much larger than individual ones of HIBCD samples. 
         [0116]    Even though we don&#39;t know exact compositions of race backgrounds, we can reasonably predict that majority of the HIBCD′ samples have European ancestry due to their USA origins. On the other hand, all most SKBCP patients have Asian ancestry. Since the KANSL1|ARL17A fusion transcripts have been detected in 35.8% of the ECD39&#39;s 39 cancer cell lines ( FIGS. 9 c  and 9 d   ) and 30% of the HIBCD&#39;s 168 samples, we can conclude that the KANSL1|ARL17A fusion transcripts and other fusion transcripts between 41 Mb and 49 Mb of chromosomal band 17q21.31 band (Table 6) can be used to detect any types of cancer and are cancer biomarkers of patients with European ancestry. Since these fusion transcripts are the consequences of “traditional” human evolutionary studies (Stefansson, et al. 2005, Rao, et al. 2010), further understanding how certain genetic types will result in fusion genes and are associated with cancer initiation, developments, uncontrolled growth, invasion, and metastasis will greatly help us to detect and prevent cancers in these subgroups of populations. 
         [0117]    Like the inversion fusion transcripts, the recurrent fusion transcripts have been observed in the interchromosomal fusion transcripts. One example is the GABBR1andUBD|PSPH fusion transcripts. The GABBR1andUBD transcription unit is located on chromosome 6 while PSPH gene is on chromosome 7. The GABBR1andUBD fusion transcripts are generally expressed at very low levels in some lymphoblastoid cell lines and have one or two copies of GABBR1andUBD|PSPH fusion transcripts. However, we have found that GABBR1andUBD|PSPH fusion transcripts are highly expressed in stem cell lines while they are expressed at various levels in many cancer lines. These data have suggested that GABBR1andUBD|PSPH fusion transcripts may play roles in promoting cell differentiation and growth. Therefore, we have then performed analysis of the 168 HIBCD breast cancer samples and 78 SKBCP breast cancer samples.  FIG. 17 a    has shown that the GABBR1andUBD|PSPH fusion transcripts have been detected in 31 breast cancer samples, which represents 18.4% of HIBCD breast cancer samples. Unlike the KANSL1|ARL17A fusion transcripts,  FIG. 17 b    has shown seven samples have been shown to have GABBR1andUBD|PSPH fusion transcripts, which represent about 10% of the SKBCP samples and are less than that found in HIBCD. The GABBR1andUBD|PSPH fusion transcripts have not been detected in normal human breast tissues and different HMEC cells. The GABBR1andUBD|PSPH expression levels, which are estimated by numbers of splice junctions per million reads (NSJMR), vary significantly among different HIBCD samples and range from 1.15×10 −2  to 8.9×10 −2 , which differ by 7.7 folds. In the future, we need to investigate whether expression levels of GABBR1andUBD|PSPH fusion transcripts are associated with cancer prognosis. 
         [0118]    As shown in  FIG. 17 , the GABBR1andUBD|PSPH fusion transcripts have been detected in many breast cancer samples. As shown in Table 4, GABBR1andUBD-PSPH fusion transcripts are expressed at very low levels. We have isolated total RNAs from BT-474 cancer cell line as described above. To verify GABBR1andUBD-PSPH fusion transcripts, we have designed primers based on the fusion transcripts as shown in Table 5. We have used these primers to amplify cDNAs to detect GABBR1andUBD|PSPH fusion transcripts. The amplified GABBR1andUBD|PSPH cDNA fragments are separated on 2.0% agarose gels. The resulted PCR fragments have been isolated and purified by Qiagen Gel Extraction Kit. The purified cDNA fragments are then cloned into pCR4-TOPO clone vector.  FIG. 18 a    has shown that interchromosomal translocations may have brought GABBR1andUBD gene on the chromosome 6 and PSPH gene of the chromosome 7 together and form a Head-Tail-to-Head structure. The putative GABBR1andUBD|PSPH fusion gene is spliced to remove introns to generate a transcript containing the first two exons of the GABBR1andUBD gene and the last exon of the PSPH gene. The amplified GABBR1andUBD|PSPH cDNA fragments are separated on 2.0% agarose gels. The resulted PCR fragment has been cloned into pCR4-TOPO clone vector and verified by DNA sequencing as shown in  FIGS. 18 b  and 18 c   . The junction sequences of fusion transcripts are verified by blast and visual inspections ( FIG. 18 c   ). Then, we have tested whether the GABBR1andUBD|PSPH fusion transcripts are presents in normal MCF10A cell line and the cancer cell lines described above. It has been negative in MCF10A and cancer cell lines. However, further experiments have shown that the GABBR1andUBD|PSPH fusion transcripts are expressed in some lymphoblastoid cell lines. However, we need to develop much faster and more accurate methods to validate these fusion transcripts. Since the fusion transcripts are shown by blast to have homologous sequences from pseudogenes or other duplications, it has not affected using them as fusion transcript markers. However, if we want to investigate the functions of the fusion transcripts, we have to use RACE PCR to get full-length sequences. 
         [0119]    As shown in Table 4, we have validated the LRRC37A3|VNN2 fusion transcripts in BT-474. 
         [0120]    Table 3 has shown that the most complex fusion events have been observed in neuroblastoma SK-N-SH cells and are ones between PVT1 oncogene and EXOC4 gene.  FIG. 19 a    shows that EXOC4 gene is located on the chromosome 7 and codes for a component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.  FIG. 19 b    shows that PVT1 oncogene is on the chromosome 8 and codes for oncogenic non-coding RNA.  FIG. 19 c    has shown that we have identified 9 PVT1|EXOC4 isoforms in SK-N-SH neuroblastoma cancer cell line.  FIG. 19 c    shows that five PVT1|EXOC4 isoforms are alternatively-spliced at the 8 th  exon of EXOC4 gene and three isoforms are alternatively-spliced at the 11 th  exon of EXOC4 gene.  FIG. 19 d    shows that PVT1|EXOC4 isoform 4 is the highest isoform and the second highest isoform is the PVT1|EXOC4 isoform 4. The remaining PVT1|EXOC4 isoforms are expressed at very low levels. Surprisingly, we have also identified EXOC4|PVT1 fusion transcripts.  FIG. 19 e    shows that we have identified four EXOC4|PVT1 fusion transcripts, all of which are alternatively spliced at the 7 th  exon of the EXOC4 gene.  FIG. 19 f    shows that EXOC4|PVT1 isoform 4 is the highest isoform and the second highest one is the EXOC4|PVT1 isoform 1 ( FIG. 19 e   ).  FIG. 19 e    shows that EXOC4|PVT1 isoform 3 and 4 differ by only three nucleotides but their expression levels differed by 11.75 folds ( FIG. 190 .  FIGS. 19 c  and 19 e    have shown that PVT1 sequences are highly variable in all PVT1|EXOC4 and EXOC4|PVT1 fusion isoforms. These suggest that all PVT1|EXOC4 and EXOC4|PVT1 fusion isoforms may be regulated differentially.  FIG. 19 g    shows that EXOC4-PVT1 gene (black bar) expression estimated by total sequence copies of supporting sequence reads is two folds of the PVT1-EXOC4 one (gray bar). 
         [0121]    In addition, in gastric cancer cell SUN16, the top two fusion transcripts are from non-coding RNA PVT1 oncogene and SLC1A2, coding for glial high affinity glutamate transporter member 2 (Table 3). These complex fusion transcripts not only provide their fusion complex gene structures, but also suggest that non-coding RNA oncogene PVT1 may play important role in cancer development. 
         [0122]    As shown in Table 3, among the top expression recurrent fusion transcripts is from MEG8 and SNORD114-1, which are located in human chromosome 14q32.2 critical region for uniparental disomy of chromosome 14 (UPD(14)) phenotypes and preferentially regulated with other imprinted genes including SNORD114-1 cluster (Charlier, et al. 2001).  FIG. 20 a    shows that a potential inversions or duplications result in reverse orders of MEG8 and SNORNA114-1 and generated SNORD114-1|MEG8 fusion gene structure. We have identified five alternatively-spliced SNORD114-1|MEG8 fusion transcripts from this genetic aberration ( FIG. 20 b   ).  FIG. 20 c    shows that the SNORD114-1|MEG8 isoform 3 is highly expressed and 100 folds higher than the isoform 5 ( FIG. 20 c   ). The SNORD114-1|MEG8 fusion transcripts have been found in A549, Daoy, LHCN-M2, M059J, SK-N-DZ, SJCRH30 and SJSA1 ( FIG. 20 d   ), the last two of which are highly expressed ( FIG. 20 e   ). Unlike all fusion genes reported so far, SNORD114-1|MEG8 fusion transcripts are fusion products between snoRNAs and non-coding RNAs and are differentially expressed in the cells ( FIG. 20 e   ). This suggests that SNORD114-1|MEG8 fusion transcripts may play some role in cancer developments. It will be important to know the exact functions of SNORD114-1|MEG8 fusion transcripts. 
         [0123]    Since this is the first time to report non-coding RNA fusion transcripts, we have performed further analysis of non-coding RNA fusion transcripts. Table 7 has shown that additional fifteen fusion transcripts have been identified, which are involved in seven putative non-coding RNA-RNA fusion genes. It is important for us to understand how these non-coding RNA-RNA fusion transcripts affected the cancer. 
         [0124]    As shown in Table 7, from the same genomic regions, we have also detected SNORD114-11|SNORD114-1 inversion fusion transcripts in numbers of cancer cell lines and some normal cell lines. These suggest that this genomic region is prone to genetic instability. Table 7 has shown that additional fifteen fusion transcripts 
         [0000]                                                                        TABLE 7                   Non-coding RNA-RNA fusion transcripts detected in cancer cells lines            5′ Genes   5′ Chr   5′ End   3′ Genes   3′ Chr   3′ Start                    ncRNA00188   17   16342728   SNHG11   20   37077373       ncRNA00188   17   16342728   SNHG7   9   139619562       ncRNA00188   17   16344444   SNHG7   9   139620868       SNHG3   1   28835417   SNHG12   1   28906099       SNHG3   1   28834672   SNHG12   1   28907158       SNHG3   1   28843379   SNHG12   1   28906493       SNHG3   1   28834672   SNORD114-1   14   101416809       SNHG3   1   28834672   SNORD1C   17   74559961       SNHG3   1   28834672   SNORD1C   17   74557480       SNORD114-11   14   101435882   MEG8   14   101402336       SNORD114-11   14   101435061   MEG8   14   101402336       SNORD114-11   14   101435882   SNORD114-1   14   101416809       SNORD114-11   14   101449879   SNORD114-1   14   101416809       SNORD114-11   14   101435882   SNORD114-1   14   101420383       SNORD114-11   14   101435061   SNORD114-1   14   101415933       SNORD114-1   14   101415933   MEG8   14   101379858       SNORD114-1   14   101422286   MEG8   14   101379858       SNORD114-1   14   101417831   MEG8   14   101402336       SNORD114-1   14   101415933   MEG8   14   101402336       SNORD114-1   14   101415933   MEG8   14   101365422                    
are involved in seven potential non-coding RNA-RNA fusion genes. It is unclear how these non-coding RNA-RNA fusion transcripts affect the cancer.
 
         [0125]    Since  FIGS. 19 and 20  have suggested that non-coding RNA fusion transcripts may play an important role in cancer developments, we have further analyzed the fusion transcripts and PFGs involved with known non-coding RNA sequences. We have identified 1074 fusion transcripts, which count for 6.5% of the total ECD39 fusion transcripts and are involved in 617 PFGs. 
         [0126]    Based on non-coding RNA functions, these fusion transcripts have been classified arbitrarily into 10 subtypes: DANCR (differentiation antagonizing non-protein coding RNA), GASS, MALTA1, miRNAs, snoRNAs, NCRNA, PVT1, SCARNA, SNHGs and TRNA (Gutschner and Diederichs 2012). DANCR (differentiation antagonizing non-protein coding RNA) codes for a 855-base-pair IncRNA, which plays in role in maintaining the undifferentiated state in somatic tissue progenitor cells. GASS (Growth Arrest-Specific 5) has played in role in promoting the apoptosis of prostate cells and growth arrest in human T-lymphocytes (Williams, et al. 2011). MALAT1 (Metastasis-associated lung adenocarcinoma transcript 1) has been implicated in implicates the ncRNA MALAT1 in regulating alternative splicing (Tripathi, et al. 2010). PVT1 is a non-coding RNA oncogene, which is the characteristic lesions associated with Burkitt lymphoma (Ghoussaini, et al. 2008). SCARNA (Small Cajal body-specific RNAs) encodes a class of small nucleolar RNAs that specifically localise to the Cajal body (Enwerem, et al. 2014). All of these RNAs has been suggested to play very important roles in various biological functions (An and Song 2011). 
         [0127]    Surprisingly, two miRNAs, MIR17HG and MIR214, have been identified in 20 fusion transcripts. MIR17HG oncogene encodes MIR17-92 cluster, which have a group of at least six miRNAs that may be involved in cell survival, proliferation, differentiation, and angiogenesis (Olive, et al. 2010, Olive, et al. 2013). MIR214 has been found to be involved in intrahepatic cholangiocarcinoma and esophageal squamous cell carcinoma and has been thought to a key hub that controls cancer networks (Penna, et al. 2015). Our analysis has shown that the oncogenic MIR17HG are fused to 9 5′ protein-coding genes while MIR214 have been found to be exclusively spliced to 8 3′ protein-coding genes. Recurrent MIR17HG-GPC5 has been detected in 10 cancer cell lines out of ECD39 cancer cell lines. These data have suggested that MIR17HG and MIR214 have played different roles in regulating these fusion transcripts. 
         [0128]      FIG. 21 a    has shown that the most abundant transcripts involved in non-coding RNAs are transcripts encoding small nucleolar RNA host (SNHG) genes, which count for 73% and 63.7% of the non-coding RNA transcripts and PFGs, respectively. These non-coding RNA fusion transcripts have been detected in 37 out of the 39 cancer cell lines ( FIG. 9 b   ). Only U251 and U2OS cell lines have no non-coding RNA fusion transcripts detected so far. This might be due to their smaller RNA-seq datasets and smaller fusion transcript datasets ( FIG. 4 a   ). 
         [0129]    As shown in  FIG. 21   b,  574 non-coding RNA fusion transcripts have been detected in K562. In contrast, only 58 fusion transcripts have been observed in SK-N-SH. The difference between the two cancer cell lines is 10 folds even though SK-N-SH has larger RNA-seq read dataset than the K562 one. This suggests that these non-coding RNA fusion transcripts are cancer cell-specific and may play important roles in cancer heterogeneity and development. 
         [0130]    As  FIG. 21 a    has shown that the most abundant non-coding RNA fusion transcripts are involved with SNHG genes, we have further analyzed the SNHG fusion transcripts.  FIG. 21 c    has shown that eight SNHG genes are found in fusion transcripts, among which SNHG3 fusion transcripts are the most abundant and count for 87% while the rest 7 SNHG genes count for only 13%. These dominant SNHG3 fusion transcripts are then classified based on the cancer cell lines.  FIG. 21 d    has shown that SNHG3 fusion transcripts have been detected in 30 different cancer lines. 
         [0131]    Consistent with results in  FIG. 21   b,  86% (573 out of 667) of the SNHG3 fusion transcripts have been found in K562. In contrast, only 6.1% (41 of 667) of them are detected in SK-N-SH and are about 14 folds less than that detected in K562. Such a high frequency of SNHG3 sequence being detected in fusion transcripts in K562 cell line strongly suggested a possibility that these fusion transcripts would constitute a natural network, which could be regulated by factors interacting with SNHG3 sequences. 
         [0132]    SNHG3 is member of the H/ACA-box class of small nucleolar RNAs (snoRNAs) and is located 9 kb upstream of RCC1 locus coding for regulator of chromosome condensation 1, 5-10% of which are read-through and generated fusion SNHG3 transcripts (Pelczar and Filipowicz 1998). 
         [0133]    It has been shown that the SNHG3 gene has been found to interact with a number of chromatin binding proteins/complexes including PRC1, PRC2, JARID1B and SUV39H1 mouse embryonic stem cells (Guttman, et al. 2011). Like most of the SNHG RNA fusion transcripts, &gt;99.99% of SNGH3 sequences are located upstream of the fusion transcripts ( FIG. 21 e   ). 
         [0134]    Since these non-coding RNA (such as SNHG3) fusion transcripts originate from one cell line, discoveries that sequences from one non-coding RNA gene are translocated to different upstream and/or downstream sequences of different genes raise possibilities that these non-coding RNA fusion transcripts can be regulated at same time by factors that recognize these non-coding RNAs. Therefore, we have proposed that these fusion transcripts by sequences from one gene constitute a natural network, which are different from those interaction networks or networks formed by protein complexes. Here, we have arbitrarily defined a 5′ natural network as sequences from a gene that have been fused to a group of upstream sequences of ≧5 different fusion transcripts. A 3′ natural network has been defined as sequences from a gene or transcriptional unit is added to downstream ≧5 different gene sequences in a cancer cell line. Since this kind of natural network can exist only within a single cell, we, first, have classified fusion transcripts based on the cell line and then classified fusion transcripts based on transcriptional units. 
         [0135]    First, we have classified the 3′ natural networks in the cancer cells. Table 8 has shown that fusion transcripts form 3′ natural networks in the different cancer cell lines. The NCBI Aceview&#39;s gene names of the complex transcriptional units (annotated ≧2 genes form one transcriptional unit) have been abbreviated. Only the first gene name of the ≧2 gene names will be shown in the tables. 
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 8 
               
             
             
               
                   
               
               
                 The 3′ natural networks formed by fusion transcripts 
               
             
          
           
               
                 5′ Genes 
                 3′ Genes 
                 5′ Chr 
                 3′ Chr 
                 Cancer Cells 
               
               
                   
               
             
          
           
               
                 C17orf70 
                 ACTG1 
                 17 
                 17 
                 A549 
               
               
                 HSPG2 
                 ACTG1 
                 1 
                 17 
                 A549 
               
               
                 P4HTM 
                 ACTG1 
                 3 
                 17 
                 A549 
               
               
                 PTPRJ 
                 ACTG1 
                 11 
                 17 
                 A549 
               
               
                 PUM2 
                 ACTG1 
                 2 
                 17 
                 A549 
               
               
                 TSPAN4 
                 ACTG1 
                 11 
                 17 
                 A549 
               
               
                 ADAT1 
                 BCAR1 
                 16 
                 16 
                 A549 
               
               
                 B4GALT1 
                 BCAR1 
                 9 
                 16 
                 A549 
               
               
                 EIF5A 
                 BCAR1 
                 17 
                 16 
                 A549 
               
               
                 SYNCRIP 
                 BCAR1 
                 6 
                 16 
                 A549 
               
               
                 ZNRF1 
                 BCAR1 
                 16 
                 16 
                 A549 
               
               
                 ARL6IP1 
                 BCAS3 
                 16 
                 17 
                 A549 
               
               
                 ASPH 
                 C9orf3 
                 8 
                 9 
                 A549 
               
               
                 ASPH 
                 C9orf3 
                 8 
                 9 
                 A549 
               
               
                 ATOH8 
                 C9orf3 
                 2 
                 9 
                 A549 
               
               
                 BAHD1 
                 C9orf3 
                 15 
                 9 
                 A549 
               
               
                 CALM2 
                 C9orf3 
                 2 
                 9 
                 A549 
               
               
                 CARS 
                 C9orf3 
                 11 
                 9 
                 A549 
               
               
                 CLPTM1 
                 C9orf3 
                 19 
                 9 
                 A549 
               
               
                 CYP24A1 
                 C9orf3 
                 20 
                 9 
                 A549 
               
               
                 EEF1D 
                 C9orf3 
                 8 
                 9 
                 A549 
               
               
                 EEF1E1 
                 C9orf3 
                 6 
                 9 
                 A549 
               
               
                 FANCC 
                 C9orf3 
                 9 
                 9 
                 A549 
               
               
                 HNRNPA2B1 
                 C9orf3 
                 7 
                 9 
                 A549 
               
               
                 HNRNPA2B1 
                 C9orf3 
                 7 
                 9 
                 A549 
               
               
                 HUWE1 
                 C9orf3 
                 23 
                 9 
                 A549 
               
               
                 HUWE1 
                 C9orf3 
                 23 
                 9 
                 A549 
               
               
                 LOC100288778 
                 C9orf3 
                 12 
                 9 
                 A549 
               
               
                 MCM7 
                 C9orf3 
                 7 
                 9 
                 A549 
               
               
                 MTA1 
                 C9orf3 
                 14 
                 9 
                 A549 
               
               
                 PRR13 
                 C9orf3 
                 12 
                 9 
                 A549 
               
               
                 PRR13 
                 C9orf3 
                 12 
                 9 
                 A549 
               
               
                 RNASEN 
                 C9orf3 
                 5 
                 9 
                 A549 
               
               
                 RNASEN 
                 C9orf3 
                 5 
                 9 
                 A549 
               
               
                 RPL23AP79 
                 C9orf3 
                 19 
                 9 
                 A549 
               
               
                 TCF25 
                 C9orf3 
                 16 
                 9 
                 A549 
               
               
                 TRAM1 
                 C9orf3 
                 8 
                 9 
                 A549 
               
               
                 TSSC4 
                 C9orf3 
                 11 
                 9 
                 A549 
               
               
                 TXN 
                 C9orf3 
                 9 
                 9 
                 A549 
               
               
                 VAV2 
                 C9orf3 
                 9 
                 9 
                 A549 
               
               
                 VRK2 
                 C9orf3 
                 2 
                 9 
                 A549 
               
               
                 C9orf46 
                 CHMP1A 
                 9 
                 16 
                 A549 
               
               
                 CPSF6 
                 CHMP1A 
                 12 
                 16 
                 A549 
               
               
                 ETFA 
                 CHMP1A 
                 15 
                 16 
                 A549 
               
               
                 FUBP1 
                 CHMP1A 
                 1 
                 16 
                 A549 
               
               
                 LOC146880 
                 CHMP1A 
                 17 
                 16 
                 A549 
               
               
                 SNX1 
                 CHMP1A 
                 15 
                 16 
                 A549 
               
               
                 ZNF595 
                 CHMP1A 
                 4 
                 16 
                 A549 
               
               
                 CALM2 
                 CTBP1 
                 2 
                 4 
                 A549 
               
               
                 CALM2 
                 CTBP1 
                 2 
                 4 
                 A549 
               
               
                 ILF3 
                 CTBP1 
                 19 
                 4 
                 A549 
               
               
                 KIAA1530 
                 CTBP1 
                 4 
                 4 
                 A549 
               
               
                 KIAA1530 
                 CTBP1 
                 4 
                 4 
                 A549 
               
               
                 NOP14 
                 CTBP1 
                 4 
                 4 
                 A549 
               
               
                 SBNO2 
                 CTBP1 
                 19 
                 4 
                 A549 
               
               
                 HNRNPH1 
                 DAZAP1 
                 5 
                 19 
                 A549 
               
               
                 NFIC 
                 DAZAP1 
                 19 
                 19 
                 A549 
               
               
                 SBNO2 
                 DAZAP1 
                 19 
                 19 
                 A549 
               
               
                 SF3A2 
                 DAZAP1 
                 19 
                 19 
                 A549 
               
               
                 STK11 
                 DAZAP1 
                 19 
                 19 
                 A549 
               
               
                 ZEB1 
                 DAZAP1 
                 10 
                 19 
                 A549 
               
               
                 C9orf3 
                 GNAS 
                 9 
                 20 
                 A549 
               
               
                 HNRNPK 
                 GNAS 
                 9 
                 20 
                 A549 
               
               
                 KYNU 
                 GNAS 
                 2 
                 20 
                 A549 
               
               
                 MTCP1NB 
                 GNAS 
                 23 
                 20 
                 A549 
               
               
                 SNHG4 
                 GNAS 
                 5 
                 20 
                 A549 
               
               
                 VAPB 
                 GNAS 
                 20 
                 20 
                 A549 
               
               
                 C17orf56 
                 MAFK 
                 17 
                 7 
                 A549 
               
               
                 CALM2 
                 MAFK 
                 2 
                 7 
                 A549 
               
               
                 DEAF1 
                 MAFK 
                 11 
                 7 
                 A549 
               
               
                 MAD1L1 
                 MAFK 
                 7 
                 7 
                 A549 
               
               
                 MAD1L1 
                 MAFK 
                 7 
                 7 
                 A549 
               
               
                 MAD1L1 
                 MAFK 
                 7 
                 7 
                 A549 
               
               
                 MICALL2 
                 MAFK 
                 7 
                 7 
                 A549 
               
               
                 SLC7A5 
                 MAFK 
                 16 
                 7 
                 A549 
               
               
                 UBASH3B 
                 MAFK 
                 11 
                 7 
                 A549 
               
               
                 APP 
                 OVOL2 
                 21 
                 20 
                 A549 
               
               
                 IDH2 
                 OVOL2 
                 15 
                 20 
                 A549 
               
               
                 ncRNA00188 
                 OVOL2 
                 17 
                 20 
                 A549 
               
               
                 PAQR5 
                 OVOL2 
                 15 
                 20 
                 A549 
               
               
                 TBC1D8 
                 OVOL2 
                 2 
                 20 
                 A549 
               
               
                 TBC1D8 
                 OVOL2 
                 2 
                 20 
                 A549 
               
               
                 TMEM138 
                 OVOL2 
                 11 
                 20 
                 A549 
               
               
                 TXNRD1 
                 OVOL2 
                 12 
                 20 
                 A549 
               
               
                 TXNRD1 
                 OVOL2 
                 12 
                 20 
                 A549 
               
               
                 COX6A1 
                 GCN1L1 
                 12 
                 12 
                 A549 
               
               
                 DCI 
                 GCN1L1 
                 16 
                 12 
                 A549 
               
               
                 MAN2C1 
                 GCN1L1 
                 15 
                 12 
                 A549 
               
               
                 PRPF8 
                 GCN1L1 
                 17 
                 12 
                 A549 
               
               
                 PXN 
                 GCN1L1 
                 12 
                 12 
                 A549 
               
               
                 SBNO1 
                 GCN1L1 
                 12 
                 12 
                 A549 
               
               
                 2-Sep 
                 GCN1L1 
                 2 
                 12 
                 A549 
               
               
                 TLN2 
                 GCN1L1 
                 15 
                 12 
                 A549 
               
               
                 TMEM116 
                 GCN1L1 
                 12 
                 12 
                 A549 
               
               
                 TMEM116 
                 GCN1L1 
                 12 
                 12 
                 A549 
               
               
                 TRAPPC4 
                 GCN1L1 
                 11 
                 12 
                 A549 
               
               
                 UBE3A 
                 GCN1L1 
                 15 
                 12 
                 A549 
               
               
                 ANKRD11 
                 SLC7A5 
                 16 
                 16 
                 A549 
               
               
                 ANKRD11 
                 SLC7A5 
                 16 
                 16 
                 A549 
               
               
                 BANP 
                 SLC7A5 
                 16 
                 16 
                 A549 
               
               
                 BANP 
                 SLC7A5 
                 16 
                 16 
                 A549 
               
               
                 KIAA0182 
                 SLC7A5 
                 16 
                 16 
                 A549 
               
               
                 KLHDC4 
                 SLC7A5 
                 16 
                 16 
                 A549 
               
               
                 KLHDC4 
                 SLC7A5 
                 16 
                 16 
                 A549 
               
               
                 KLHDC4 
                 SLC7A5 
                 16 
                 16 
                 A549 
               
               
                 C7orf44 
                 SUN1 
                 7 
                 7 
                 A549 
               
               
                 C7orf50 
                 SUN1 
                 7 
                 7 
                 A549 
               
               
                 EIF4EBP2 
                 SUN1 
                 10 
                 7 
                 A549 
               
               
                 HEATR2 
                 SUN1 
                 7 
                 7 
                 A549 
               
               
                 HNRNPF 
                 SUN1 
                 10 
                 7 
                 A549 
               
               
                 MICALL2 
                 SUN1 
                 7 
                 7 
                 A549 
               
               
                 PRKAR1B 
                 SUN1 
                 7 
                 7 
                 A549 
               
               
                 PRKAR1B 
                 SUN1 
                 7 
                 7 
                 A549 
               
               
                 AKT1 
                 TSPAN4 
                 14 
                 11 
                 A549 
               
               
                 CALM2 
                 TSPAN4 
                 2 
                 11 
                 A549 
               
               
                 CHID1 
                 TSPAN4 
                 11 
                 11 
                 A549 
               
               
                 COL5A1 
                 TSPAN4 
                 9 
                 11 
                 A549 
               
               
                 EEF1D 
                 TSPAN4 
                 8 
                 11 
                 A549 
               
               
                 FBF1 
                 TSPAN4 
                 17 
                 11 
                 A549 
               
               
                 HNRNPC 
                 TSPAN4 
                 14 
                 11 
                 A549 
               
               
                 MED13L 
                 TSPAN4 
                 12 
                 11 
                 A549 
               
               
                 PPP1R12C 
                 TSPAN4 
                 19 
                 11 
                 A549 
               
               
                 PPP6R2 
                 TSPAN4 
                 22 
                 11 
                 A549 
               
               
                 RGS20 
                 TSPAN4 
                 8 
                 11 
                 A549 
               
               
                 SETD8 
                 TSPAN4 
                 12 
                 11 
                 A549 
               
               
                 SHANK3 
                 TSPAN4 
                 22 
                 11 
                 A549 
               
               
                 TOB1 
                 TSPAN4 
                 17 
                 11 
                 A549 
               
               
                 UCKL1 
                 TSPAN4 
                 20 
                 11 
                 A549 
               
               
                 DDX5 
                 UBC 
                 17 
                 12 
                 A549 
               
               
                 KRT80 
                 UBC 
                 12 
                 12 
                 A549 
               
               
                 NCOR2 
                 UBC 
                 12 
                 12 
                 A549 
               
               
                 NCOR2 
                 UBC 
                 12 
                 12 
                 A549 
               
               
                 NCOR2 
                 UBC 
                 12 
                 12 
                 A549 
               
               
                 NCOR2 
                 UBC 
                 12 
                 12 
                 A549 
               
               
                 ORAOV1 
                 UBC 
                 11 
                 12 
                 A549 
               
               
                 UHRF1BP1L 
                 UBC 
                 12 
                 12 
                 A549 
               
               
                 ZNRD1 
                 UBC 
                 6 
                 12 
                 A549 
               
               
                 ABCC3 
                 ZNF598 
                 17 
                 16 
                 A549 
               
               
                 E4F1 
                 ZNF598 
                 16 
                 16 
                 A549 
               
               
                 EEF1D 
                 ZNF598 
                 8 
                 16 
                 A549 
               
               
                 TECPR1 
                 ZNF598 
                 7 
                 16 
                 A549 
               
               
                 SNHG3 
                 ZNF638 
                 1 
                 2 
                 A549 
               
               
                 ACAD10 
                 GNAS 
                 12 
                 20 
                 CUTLL 
               
               
                 GEN1 
                 GNAS 
                 2 
                 20 
                 CUTLL 
               
               
                 HNRNPH1 
                 GNAS 
                 5 
                 20 
                 CUTLL 
               
               
                 MYL6B 
                 GNAS 
                 12 
                 20 
                 CUTLL 
               
               
                 SLMO2 
                 GNAS 
                 20 
                 20 
                 CUTLL 
               
               
                 HNRNPF 
                 DAZAP1 
                 10 
                 19 
                 Hela-3 
               
               
                 HNRNPF 
                 DAZAP1 
                 10 
                 19 
                 Hela-3 
               
               
                 NDUFS7 
                 DAZAP1 
                 19 
                 19 
                 Hela-3 
               
               
                 NFIC 
                 DAZAP1 
                 19 
                 19 
                 Hela-3 
               
               
                 PPP1R12C 
                 DAZAP1 
                 19 
                 19 
                 Hela-3 
               
               
                 PPP1R12C 
                 DAZAP1 
                 19 
                 19 
                 Hela-3 
               
               
                 RPL22 
                 DAZAP1 
                 1 
                 19 
                 Hela-3 
               
               
                 SBNO2 
                 DAZAP1 
                 19 
                 19 
                 Hela-3 
               
               
                 SULT1A1 
                 DAZAP1 
                 16 
                 19 
                 Hela-3 
               
               
                 ANKRD11 
                 FAM156B 
                 16 
                 23 
                 Hela-3 
               
               
                 FAM156A 
                 FAM156B 
                 23 
                 23 
                 Hela-3 
               
               
                 KANK2 
                 FAM156B 
                 19 
                 23 
                 Hela-3 
               
               
                 RASA4P 
                 FAM156B 
                 7 
                 23 
                 Hela-3 
               
               
                 SLC6A15 
                 FAM156B 
                 12 
                 23 
                 Hela-3 
               
               
                 PLEKHB2 
                 FAM168B 
                 2 
                 2 
                 Hela-3 
               
               
                 ASAP1 
                 GNAS 
                 8 
                 20 
                 Hela-3 
               
               
                 BRCA1P1 
                 GNAS 
                 17 
                 20 
                 Hela-3 
               
               
                 CBX5 
                 GNAS 
                 12 
                 20 
                 Hela-3 
               
               
                 GEN1 
                 GNAS 
                 2 
                 20 
                 Hela-3 
               
               
                 HUWE1 
                 GNAS 
                 23 
                 20 
                 Hela-3 
               
               
                 KIAA0182 
                 GNAS 
                 16 
                 20 
                 Hela-3 
               
               
                 KYNU 
                 GNAS 
                 2 
                 20 
                 Hela-3 
               
               
                 SLMO2 
                 GNAS 
                 20 
                 20 
                 Hela-3 
               
               
                 SNHG3 
                 GNAS 
                 1 
                 20 
                 Hela-3 
               
               
                 TP53 
                 GNAS 
                 17 
                 20 
                 Hela-3 
               
               
                 C5 
                 FN1 
                 9 
                 2 
                 HepG2 
               
               
                 HNRNPH1 
                 FN1 
                 5 
                 2 
                 HepG2 
               
               
                 NAA35 
                 FN1 
                 9 
                 2 
                 HepG2 
               
               
                 RPL31 
                 FN1 
                 2 
                 2 
                 HepG2 
               
               
                 RPL31 
                 FN1 
                 2 
                 2 
                 HepG2 
               
               
                 SNHG3 
                 FN1 
                 1 
                 2 
                 HepG2 
               
               
                 SNHG3 
                 FN1 
                 1 
                 2 
                 HepG2 
               
               
                 TTC15 
                 FN1 
                 2 
                 2 
                 HepG2 
               
               
                 ARF1 
                 GNAS 
                 1 
                 20 
                 HepG2 
               
               
                 B2M 
                 GNAS 
                 15 
                 20 
                 HepG2 
               
               
                 CBX5 
                 GNAS 
                 12 
                 20 
                 HepG2 
               
               
                 EEF1D 
                 GNAS 
                 8 
                 20 
                 HepG2 
               
               
                 HNRNPH1 
                 GNAS 
                 5 
                 20 
                 HepG2 
               
               
                 KPNA6 
                 GNAS 
                 1 
                 20 
                 HepG2 
               
               
                 MGA 
                 GNAS 
                 15 
                 20 
                 HepG2 
               
               
                 SLMO2 
                 GNAS 
                 20 
                 20 
                 HepG2 
               
               
                 STAG2 
                 GNAS 
                 23 
                 20 
                 HepG2 
               
               
                 ANKRD11 
                 OVOL2 
                 16 
                 20 
                 HepG2 
               
               
                 APP 
                 OVOL2 
                 21 
                 20 
                 HepG2 
               
               
                 JUB 
                 OVOL2 
                 14 
                 20 
                 HepG2 
               
               
                 TASP1 
                 OVOL2 
                 20 
                 20 
                 HepG2 
               
               
                 ZNF133 
                 OVOL2 
                 20 
                 20 
                 HepG2 
               
               
                 ZNF519 
                 OVOL2 
                 18 
                 20 
                 HepG2 
               
               
                 CHD6 
                 GNAS 
                 20 
                 20 
                 HT29 
               
               
                 CORO7 
                 GNAS 
                 16 
                 20 
                 HT29 
               
               
                 DNAJB6 
                 GNAS 
                 7 
                 20 
                 HT29 
               
               
                 RPL12P27 
                 GNAS 
                 10 
                 20 
                 HT29 
               
               
                 RSU1 
                 GNAS 
                 10 
                 20 
                 HT29 
               
               
                 C7orf50 
                 MAD1L1 
                 7 
                 7 
                 HT29 
               
               
                 NFE2L3 
                 MAD1L1 
                 7 
                 7 
                 HT29 
               
               
                 TTYH3 
                 MAD1L1 
                 7 
                 7 
                 HT29 
               
               
                 UBAP1 
                 MAD1L1 
                 9 
                 7 
                 HT29 
               
               
                 ZNF766 
                 MAD1L1 
                 19 
                 7 
                 HT29 
               
               
                 HNRNPH1 
                 CANX 
                 5 
                 5 
                 K562 
               
               
                 MAPK9 
                 CANX 
                 5 
                 5 
                 K562 
               
               
                 PPFIA1 
                 CANX 
                 11 
                 5 
                 K562 
               
               
                 SNHG3 
                 CANX 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 CANX 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 CANX 
                 1 
                 5 
                 K562 
               
               
                 SQSTM1 
                 CANX 
                 5 
                 5 
                 K562 
               
               
                 SQSTM1 
                 CANX 
                 5 
                 5 
                 K562 
               
               
                 KIAA1530 
                 CTBP1 
                 4 
                 4 
                 K562 
               
               
                 LOC100129917 
                 CTBP1 
                 4 
                 4 
                 K562 
               
               
                 MAEA 
                 CTBP1 
                 4 
                 4 
                 K562 
               
               
                 OAZ1 
                 CTBP1 
                 19 
                 4 
                 K562 
               
               
                 PCGF3 
                 CTBP1 
                 4 
                 4 
                 K562 
               
               
                 PCGF3 
                 CTBP1 
                 4 
                 4 
                 K562 
               
               
                 SPON2 
                 CTBP1 
                 4 
                 4 
                 K562 
               
               
                 ASH1L 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 C14orf156 
                 DAP3 
                 14 
                 1 
                 K562 
               
               
                 C14orf156 
                 DAP3 
                 14 
                 1 
                 K562 
               
               
                 GON4L 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 GON4L 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 SSR2 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 IVNS1ABP 
                 EIF3E 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 EIF3E 
                 1 
                 8 
                 K562 
               
               
                 ST3GAL1 
                 EIF3E 
                 8 
                 8 
                 K562 
               
               
                 ST3GAL1 
                 EIF3E 
                 8 
                 8 
                 K562 
               
               
                 TTC35 
                 EIF3E 
                 8 
                 8 
                 K562 
               
               
                 XRCC4 
                 EIF3E 
                 5 
                 8 
                 K562 
               
               
                 CHCHD3 
                 FAF1 
                 7 
                 1 
                 K562 
               
               
                 CHCHD3 
                 FAF1 
                 7 
                 1 
                 K562 
               
               
                 KIAA0114 
                 FAF1 
                 4 
                 1 
                 K562 
               
               
                 MIR17HG 
                 FAF1 
                 13 
                 1 
                 K562 
               
               
                 OSBPL9 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 OSBPL9 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 RNF11 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 RNF11 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 RNF11 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG5 
                 FAF1 
                 6 
                 1 
                 K562 
               
               
                 SNORD1C 
                 FAF1 
                 17 
                 1 
                 K562 
               
               
                 TM2D1 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 C10orf18 
                 GDI2 
                 10 
                 10 
                 K562 
               
               
                 C10orf18 
                 GDI2 
                 10 
                 10 
                 K562 
               
               
                 NET1 
                 GDI2 
                 10 
                 10 
                 K562 
               
               
                 PFKFB3 
                 GDI2 
                 10 
                 10 
                 K562 
               
               
                 POLR2D 
                 GDI2 
                 2 
                 10 
                 K562 
               
               
                 RBM17 
                 GDI2 
                 10 
                 10 
                 K562 
               
               
                 SNHG3 
                 GDI2 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 GDI2 
                 1 
                 10 
                 K562 
               
               
                 WDR37 
                 GDI2 
                 10 
                 10 
                 K562 
               
               
                 ABO 
                 GNAS 
                 9 
                 20 
                 K562 
               
               
                 ACAD10 
                 GNAS 
                 12 
                 20 
                 K562 
               
               
                 ARHGEF2 
                 GNAS 
                 1 
                 20 
                 K562 
               
               
                 BCOR 
                 GNAS 
                 23 
                 20 
                 K562 
               
               
                 FAM49B 
                 GNAS 
                 8 
                 20 
                 K562 
               
               
                 FAM60A 
                 GNAS 
                 12 
                 20 
                 K562 
               
               
                 HDLBP 
                 GNAS 
                 2 
                 20 
                 K562 
               
               
                 ITCH 
                 GNAS 
                 20 
                 20 
                 K562 
               
               
                 KIAA0182 
                 GNAS 
                 16 
                 20 
                 K562 
               
               
                 MIPOL1 
                 GNAS 
                 14 
                 20 
                 K562 
               
               
                 NFYC 
                 GNAS 
                 1 
                 20 
                 K562 
               
               
                 NOC4L 
                 GNAS 
                 12 
                 20 
                 K562 
               
               
                 SHB 
                 GNAS 
                 9 
                 20 
                 K562 
               
               
                 SNHG4 
                 GNAS 
                 5 
                 20 
                 K562 
               
               
                 TYMS 
                 GNAS 
                 18 
                 20 
                 K562 
               
               
                 ROD1 
                 KIAA0368 
                 9 
                 9 
                 K562 
               
               
                 SUSD1 
                 KIAA0368 
                 9 
                 9 
                 K562 
               
               
                 SUSD1 
                 KIAA0368 
                 9 
                 9 
                 K562 
               
               
                 TXN 
                 KIAA0368 
                 9 
                 9 
                 K562 
               
               
                 UGCG 
                 KIAA0368 
                 9 
                 9 
                 K562 
               
               
                 UGCG 
                 KIAA0368 
                 9 
                 9 
                 K562 
               
               
                 VPS13A 
                 KIAA0368 
                 9 
                 9 
                 K562 
               
               
                 RCSD1 
                 PDS5A 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 PDS5A 
                 1 
                 4 
                 K562 
               
               
                 TMEM165 
                 PDS5A 
                 4 
                 4 
                 K562 
               
               
                 UBE2K 
                 PDS5A 
                 4 
                 4 
                 K562 
               
               
                 UBE2K 
                 PDS5A 
                 4 
                 4 
                 K562 
               
               
                 USP34 
                 PDS5A 
                 2 
                 4 
                 K562 
               
               
                 ARL4A 
                 PHF14 
                 7 
                 7 
                 K562 
               
               
                 KIAA0114 
                 PHF14 
                 4 
                 7 
                 K562 
               
               
                 ncRNA00188 
                 PHF14 
                 17 
                 7 
                 K562 
               
               
                 ncRNA00188 
                 PHF14 
                 17 
                 7 
                 K562 
               
               
                 NDUFA4 
                 PHF14 
                 7 
                 7 
                 K562 
               
               
                 SNHG3 
                 PHF14 
                 1 
                 7 
                 K562 
               
               
                 VWDE 
                 PHF14 
                 7 
                 7 
                 K562 
               
               
                 VWDE 
                 PHF14 
                 7 
                 7 
                 K562 
               
               
                 C11orf73 
                 PICALM 
                 11 
                 11 
                 K562 
               
               
                 C11orf73 
                 PICALM 
                 11 
                 11 
                 K562 
               
               
                 COPB2 
                 PICALM 
                 3 
                 11 
                 K562 
               
               
                 COPB2 
                 PICALM 
                 3 
                 11 
                 K562 
               
               
                 EED 
                 PICALM 
                 11 
                 11 
                 K562 
               
               
                 FDXACB1 
                 PICALM 
                 11 
                 11 
                 K562 
               
               
                 KIAA0114 
                 PICALM 
                 4 
                 11 
                 K562 
               
               
                 KIF2A 
                 PICALM 
                 5 
                 11 
                 K562 
               
               
                 RPS20 
                 PICALM 
                 8 
                 11 
                 K562 
               
               
                 RPS20 
                 PICALM 
                 8 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG4 
                 PICALM 
                 5 
                 11 
                 K562 
               
               
                 SNHG4 
                 PICALM 
                 5 
                 11 
                 K562 
               
               
                 TAF1 
                 PICALM 
                 11 
                 11 
                 K562 
               
               
                 TAF1 
                 PICALM 
                 11 
                 11 
                 K562 
               
               
                 TMEM126B 
                 PICALM 
                 11 
                 11 
                 K562 
               
               
                 ZNF33B 
                 PICALM 
                 10 
                 11 
                 K562 
               
               
                 AGPAT5 
                 PRKCB 
                 8 
                 16 
                 K562 
               
               
                 AGPAT5 
                 PRKCB 
                 8 
                 16 
                 K562 
               
               
                 C15orf26 
                 PRKCB 
                 15 
                 16 
                 K562 
               
               
                 C15orf26 
                 PRKCB 
                 15 
                 16 
                 K562 
               
               
                 KIAA0114 
                 PRKCB 
                 4 
                 16 
                 K562 
               
               
                 KIAA0114 
                 PRKCB 
                 4 
                 16 
                 K562 
               
               
                 SNHG3 
                 PRKCB 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 PRKCB 
                 1 
                 16 
                 K562 
               
               
                 ACOX3 
                 PSMB1 
                 4 
                 6 
                 K562 
               
               
                 CTBP2 
                 PSMB1 
                 10 
                 6 
                 K562 
               
               
                 HGS 
                 PSMB1 
                 17 
                 6 
                 K562 
               
               
                 MLL5 
                 PSMB1 
                 7 
                 6 
                 K562 
               
               
                 PAOX 
                 PSMB1 
                 10 
                 6 
                 K562 
               
               
                 WDR27 
                 PSMB1 
                 6 
                 6 
                 K562 
               
               
                 ZDHHC14 
                 PSMB1 
                 6 
                 6 
                 K562 
               
               
                 TWSG1 
                 RALBP1 
                 18 
                 18 
                 K562 
               
               
                 ARHGEF18 
                 RANBP1 
                 19 
                 22 
                 K562 
               
               
                 BOP1 
                 RANBP1 
                 8 
                 22 
                 K562 
               
               
                 C22orf25 
                 RANBP1 
                 22 
                 22 
                 K562 
               
               
                 C22orf25 
                 RANBP1 
                 22 
                 22 
                 K562 
               
               
                 EIF5A 
                 RANBP1 
                 17 
                 22 
                 K562 
               
               
                 KLHL22 
                 RANBP1 
                 22 
                 22 
                 K562 
               
               
                 MED15 
                 RANBP1 
                 22 
                 22 
                 K562 
               
               
                 RPS8 
                 RANBP1 
                 1 
                 22 
                 K562 
               
               
                 RPS8 
                 RANBP1 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 RANBP1 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 RANBP1 
                 1 
                 22 
                 K562 
               
               
                 VRK2 
                 RANBP1 
                 2 
                 22 
                 K562 
               
               
                 WHSC2 
                 RANBP1 
                 4 
                 22 
                 K562 
               
               
                 WHSC2 
                 RANBP1 
                 4 
                 22 
                 K562 
               
               
                 VMAC 
                 RANBP3 
                 19 
                 19 
                 K562 
               
               
                 HIVEP1 
                 RANBP9 
                 6 
                 6 
                 K562 
               
               
                 GNL3 
                 RNF149 
                 3 
                 2 
                 K562 
               
               
                 RPL10 
                 RNF149 
                 23 
                 2 
                 K562 
               
               
                 RPL17A 
                 RNF149 
                 9 
                 2 
                 K562 
               
               
                 RPL27A 
                 RNF149 
                 11 
                 2 
                 K562 
               
               
                 RPL3 
                 RNF149 
                 22 
                 2 
                 K562 
               
               
                 SCARNA17 
                 RNF149 
                 18 
                 2 
                 K562 
               
               
                 SNHG3 
                 RNF149 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 RNF149 
                 1 
                 2 
                 K562 
               
               
                 LARP4 
                 GCN1L1 
                 12 
                 12 
                 K562 
               
               
                 NOP2 
                 GCN1L1 
                 12 
                 12 
                 K562 
               
               
                 NUP210 
                 GCN1L1 
                 3 
                 12 
                 K562 
               
               
                 SBNO1 
                 GCN1L1 
                 12 
                 12 
                 K562 
               
               
                 TMEM138 
                 GCN1L1 
                 11 
                 12 
                 K562 
               
               
                 HERC1 
                 RPS27A 
                 15 
                 2 
                 K562 
               
               
                 KLF1 
                 RPS27A 
                 19 
                 2 
                 K562 
               
               
                 RPL27A 
                 RPS27A 
                 11 
                 2 
                 K562 
               
               
                 RPL27A 
                 RPS27A 
                 11 
                 2 
                 K562 
               
               
                 RPS3 
                 RPS27A 
                 11 
                 2 
                 K562 
               
               
                 SNHG4 
                 RPS27A 
                 5 
                 2 
                 K562 
               
               
                 SNHG4 
                 RPS27A 
                 5 
                 2 
                 K562 
               
               
                 SPTBN1 
                 RPS27A 
                 2 
                 2 
                 K562 
               
               
                 SRP9 
                 RPS27A 
                 1 
                 2 
                 K562 
               
               
                 TOMM20 
                 RPS27A 
                 1 
                 2 
                 K562 
               
               
                 ncRNA00188 
                 RPS3 
                 17 
                 11 
                 K562 
               
               
                 ncRNA00188 
                 RPS3 
                 17 
                 11 
                 K562 
               
               
                 RPL27A 
                 RPS3 
                 11 
                 11 
                 K562 
               
               
                 SNHG3 
                 RPS3 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 RPS3 
                 1 
                 11 
                 K562 
               
               
                 AFF1 
                 SIKE1 
                 4 
                 1 
                 K562 
               
               
                 AK2 
                 SIKE1 
                 1 
                 1 
                 K562 
               
               
                 BAZ1A 
                 SIKE1 
                 14 
                 1 
                 K562 
               
               
                 CAPZA1 
                 SIKE1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SIKE1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SIKE1 
                 1 
                 1 
                 K562 
               
               
                 TRIM33 
                 SIKE1 
                 1 
                 1 
                 K562 
               
               
                 BAHD1 
                 UBB 
                 15 
                 17 
                 K562 
               
               
                 CAPZA1 
                 UBB 
                 1 
                 17 
                 K562 
               
               
                 CAPZA2 
                 UBB 
                 7 
                 17 
                 K562 
               
               
                 EEF1A1 
                 UBB 
                 6 
                 17 
                 K562 
               
               
                 IL23R 
                 UBB 
                 1 
                 17 
                 K562 
               
               
                 LARP4 
                 UBB 
                 12 
                 17 
                 K562 
               
               
                 MYL6B 
                 UBB 
                 12 
                 17 
                 K562 
               
               
                 PI4KA 
                 UBB 
                 22 
                 17 
                 K562 
               
               
                 RAI1 
                 UBB 
                 17 
                 17 
                 K562 
               
               
                 RASA4P 
                 UBB 
                 7 
                 17 
                 K562 
               
               
                 RPL15 
                 UBB 
                 3 
                 17 
                 K562 
               
               
                 RPL15 
                 UBB 
                 3 
                 17 
                 K562 
               
               
                 RPS3 
                 UBB 
                 11 
                 7 
                 K562 
               
               
                 SNHG3 
                 UBB 
                 1 
                 17 
                 K562 
               
               
                 CRAMP1L 
                 UBE2I 
                 16 
                 16 
                 K562 
               
               
                 LMF1 
                 UBE2I 
                 16 
                 16 
                 K562 
               
               
                 SNHG3 
                 UBE2I 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 UBE2I 
                 1 
                 16 
                 K562 
               
               
                 SOLH 
                 UBE2I 
                 16 
                 16 
                 K562 
               
               
                 SOLH 
                 UBE2I 
                 16 
                 16 
                 K562 
               
               
                 WHSC1 
                 UBE2I 
                 4 
                 16 
                 K562 
               
               
                 ABCC5 
                 STAMBP 
                 3 
                 2 
                 LHCN-M2 
               
               
                 ADAMTS2 
                 STAMBP 
                 5 
                 2 
                 LHCN-M2 
               
               
                 ANKRD11 
                 STAMBP 
                 16 
                 2 
                 LHCN-M2 
               
               
                 BCL2L11 
                 STAMBP 
                 2 
                 2 
                 LHCN-M2 
               
               
                 BLCAP 
                 STAMBP 
                 20 
                 2 
                 LHCN-M2 
               
               
                 C7orf13 
                 STAMBP 
                 7 
                 2 
                 LHCN-M2 
               
               
                 CABLES1 
                 STAMBP 
                 18 
                 2 
                 LHCN-M2 
               
               
                 CALM2 
                 STAMBP 
                 2 
                 2 
                 LHCN-M2 
               
               
                 CAPN2 
                 STAMBP 
                 1 
                 2 
                 LHCN-M2 
               
               
                 CCDC46 
                 STAMBP 
                 17 
                 2 
                 LHCN-M2 
               
               
                 CCDC55 
                 STAMBP 
                 17 
                 2 
                 LHCN-M2 
               
               
                 CHFR 
                 STAMBP 
                 12 
                 2 
                 LHCN-M2 
               
               
                 CLK3 
                 STAMBP 
                 15 
                 2 
                 LHCN-M2 
               
               
                 COL3A1 
                 STAMBP 
                 2 
                 2 
                 LHCN-M2 
               
               
                 CWC22 
                 STAMBP 
                 2 
                 2 
                 LHCN-M2 
               
               
                 DECR1 
                 STAMBP 
                 8 
                 2 
                 LHCN-M2 
               
               
                 ERP44 
                 STAMBP 
                 9 
                 2 
                 LHCN-M2 
               
               
                 FRYL 
                 STAMBP 
                 4 
                 2 
                 LHCN-M2 
               
               
                 FRYL 
                 STAMBP 
                 4 
                 2 
                 LHCN-M2 
               
               
                 GAS6 
                 STAMBP 
                 13 
                 2 
                 LHCN-M2 
               
               
                 HDAC5 
                 STAMBP 
                 17 
                 2 
                 LHCN-M2 
               
               
                 HNRNPK 
                 STAMBP 
                 9 
                 2 
                 LHCN-M2 
               
               
                 KDM6A 
                 STAMBP 
                 23 
                 2 
                 LHCN-M2 
               
               
                 KLF5 
                 STAMBP 
                 13 
                 2 
                 LHCN-M2 
               
               
                 KLHL29 
                 STAMBP 
                 2 
                 2 
                 LHCN-M2 
               
               
                 LDLRAD3 
                 STAMBP 
                 11 
                 2 
                 LHCN-M2 
               
               
                 LOC100129917 
                 STAMBP 
                 4 
                 2 
                 LHCN-M2 
               
               
                 LRRC28 
                 STAMBP 
                 15 
                 2 
                 LHCN-M2 
               
               
                 LSP1 
                 STAMBP 
                 11 
                 2 
                 LHCN-M2 
               
               
                 MAD1L1 
                 STAMBP 
                 7 
                 2 
                 LHCN-M2 
               
               
                 MBD2 
                 STAMBP 
                 18 
                 2 
                 LHCN-M2 
               
               
                 MED8 
                 STAMBP 
                 1 
                 2 
                 LHCN-M2 
               
               
                 MTMR3 
                 STAMBP 
                 22 
                 2 
                 LHCN-M2 
               
               
                 NAPG 
                 STAMBP 
                 18 
                 2 
                 LHCN-M2 
               
               
                 PCDH9 
                 STAMBP 
                 13 
                 2 
                 LHCN-M2 
               
               
                 PCDHG 
                 STAMBP 
                 5 
                 2 
                 LHCN-M2 
               
               
                 PCDHG 
                 STAMBP 
                 5 
                 2 
                 LHCN-M2 
               
               
                 PICALM 
                 STAMBP 
                 11 
                 2 
                 LHCN-M2 
               
               
                 POFUT2 
                 STAMBP 
                 21 
                 2 
                 LHCN-M2 
               
               
                 PRMT2 
                 STAMBP 
                 21 
                 2 
                 LHCN-M2 
               
               
                 PRMT2 
                 STAMBP 
                 21 
                 2 
                 LHCN-M2 
               
               
                 RELT 
                 STAMBP 
                 11 
                 2 
                 LHCN-M2 
               
               
                 RGS20 
                 STAMBP 
                 8 
                 2 
                 LHCN-M2 
               
               
                 RUNX1 
                 STAMBP 
                 21 
                 2 
                 LHCN-M2 
               
               
                 11-Sep 
                 STAMBP 
                 4 
                 2 
                 LHCN-M2 
               
               
                 SLC38A10 
                 STAMBP 
                 17 
                 2 
                 LHCN-M2 
               
               
                 TMEM87B 
                 STAMBP 
                 2 
                 2 
                 LHCN-M2 
               
               
                 TSPAN3 
                 STAMBP 
                 15 
                 2 
                 LHCN-M2 
               
               
                 TUBA1A 
                 STAMBP 
                 12 
                 2 
                 LHCN-M2 
               
               
                 UAP1 
                 STAMBP 
                 1 
                 2 
                 LHCN-M2 
               
               
                 UBE3C 
                 STAMBP 
                 7 
                 2 
                 LHCN-M2 
               
               
                 WDR37 
                 STAMBP 
                 10 
                 2 
                 LHCN-M2 
               
               
                 WHSC2 
                 STAMBP 
                 4 
                 2 
                 LHCN-M2 
               
               
                 XPO4 
                 STAMBP 
                 13 
                 2 
                 LHCN-M2 
               
               
                 ZFP106 
                 STAMBP 
                 15 
                 2 
                 LHCN-M2 
               
               
                 ZNF24 
                 STAMBP 
                 18 
                 2 
                 LHCN-M2 
               
               
                 ZNF556 
                 STAMBP 
                 19 
                 2 
                 LHCN-M2 
               
               
                 ZNF571 
                 STAMBP 
                 19 
                 2 
                 LHCN-M2 
               
               
                 ZNF702P 
                 STAMBP 
                 19 
                 2 
                 LHCN-M2 
               
               
                 CAPRIN1 
                 CHMP1A 
                 11 
                 16 
                 MCF7 
               
               
                 CYP24A1 
                 CHMP1A 
                 20 
                 16 
                 MCF7 
               
               
                 DCP1B 
                 CHMP1A 
                 12 
                 16 
                 MCF7 
               
               
                 ING3 
                 CHMP1A 
                 7 
                 16 
                 MCF7 
               
               
                 LMBR1 
                 CHMP1A 
                 7 
                 16 
                 MCF7 
               
               
                 POLD3 
                 CHMP1A 
                 11 
                 16 
                 MCF7 
               
               
                 POLD3 
                 CHMP1A 
                 11 
                 16 
                 MCF7 
               
               
                 RBL2 
                 CHMP1A 
                 16 
                 16 
                 MCF7 
               
               
                 ZNF286A 
                 CHMP1A 
                 17 
                 16 
                 MCF7 
               
               
                 ZNF519 
                 CHMP1A 
                 18 
                 16 
                 MCF7 
               
               
                 CCDC57 
                 CHMP4B 
                 17 
                 20 
                 MCF7 
               
               
                 RALY 
                 CHMP4B 
                 20 
                 20 
                 MCF7 
               
               
                 DDX5 
                 GNAI3 
                 17 
                 1 
                 MCF7 
               
               
                 NR2F2 
                 GNAI3 
                 15 
                 1 
                 MCF7 
               
               
                 SYCP2 
                 GNAI3 
                 20 
                 1 
                 MCF7 
               
               
                 TANC2 
                 GNAI3 
                 17 
                 1 
                 MCF7 
               
               
                 TNS3 
                 GNAI3 
                 7 
                 1 
                 MCF7 
               
               
                 CTBP2 
                 GNAS 
                 10 
                 20 
                 MCF7 
               
               
                 EEF1D 
                 GNAS 
                 8 
                 20 
                 MCF7 
               
               
                 KIAA0114 
                 GNAS 
                 4 
                 20 
                 MCF7 
               
               
                 MGA 
                 GNAS 
                 15 
                 20 
                 MCF7 
               
               
                 NCOA3 
                 GNAS 
                 20 
                 20 
                 MCF7 
               
               
                 SNHG3 
                 GNAS 
                 1 
                 20 
                 MCF7 
               
               
                 TYMS 
                 GNAS 
                 18 
                 20 
                 MCF7 
               
               
                 YWHAE 
                 GNAS 
                 17 
                 20 
                 MCF7 
               
               
                 ATP5I 
                 ZNF595 
                 4 
                 4 
                 MCF7 
               
               
                 HSPD1 
                 ZNF595 
                 2 
                 4 
                 MCF7 
               
               
                 IKBKAP 
                 ZNF595 
                 9 
                 4 
                 MCF7 
               
               
                 TOM1L2 
                 ZNF595 
                 17 
                 4 
                 MCF7 
               
               
                 TRMT2B 
                 ZNF595 
                 23 
                 4 
                 MCF7 
               
               
                 FSTL5 
                 MRPL21 
                 4 
                 11 
                 SK-Mel-5 
               
               
                 ncRNA00188 
                 MRPL21 
                 17 
                 11 
                 SK-Mel-5 
               
               
                 NOP56 
                 MRPL21 
                 20 
                 11 
                 SK-Mel-5 
               
               
                 RAB38 
                 MRPL21 
                 11 
                 11 
                 SK-Mel-5 
               
               
                 TUBD1 
                 MRPL21 
                 17 
                 11 
                 SK-Mel-5 
               
               
                 ATP6V1G2 
                 MRPL52 
                 6 
                 14 
                 SK-Mel-5 
               
               
                 ASPH 
                 CHMP1A 
                 8 
                 16 
                 SK-N-DZ 
               
               
                 CCDC64 
                 CHMP1A 
                 12 
                 16 
                 SK-N-DZ 
               
               
                 HECTD2 
                 CHMP1A 
                 10 
                 16 
                 SK-N-DZ 
               
               
                 ISCA1 
                 CHMP1A 
                 9 
                 16 
                 SK-N-DZ 
               
               
                 RIMBP2 
                 CHMP1A 
                 12 
                 16 
                 SK-N-DZ 
               
               
                 TMEM165 
                 CHMP1A 
                 4 
                 16 
                 SK-N-DZ 
               
               
                 ZNF726 
                 CHMP1A 
                 19 
                 16 
                 SK-N-DZ 
               
               
                 ZNF738 
                 CHMP1A 
                 19 
                 16 
                 SK-N-DZ 
               
               
                 ATP5I 
                 DDX1 
                 4 
                 2 
                 SK-N-DZ 
               
               
                 DCAKD 
                 DDX1 
                 17 
                 2 
                 SK-N-DZ 
               
               
                 EIF3A 
                 DDX1 
                 10 
                 2 
                 SK-N-DZ 
               
               
                 MANEA 
                 DDX1 
                 6 
                 2 
                 SK-N-DZ 
               
               
                 MED28 
                 DDX1 
                 4 
                 2 
                 SK-N-DZ 
               
               
                 NBAS 
                 DDX1 
                 2 
                 2 
                 SK-N-DZ 
               
               
                 NBAS 
                 DDX1 
                 2 
                 2 
                 SK-N-DZ 
               
               
                 RPS12 
                 DDX1 
                 6 
                 2 
                 SK-N-DZ 
               
               
                 SRRM1 
                 DDX1 
                 1 
                 2 
                 SK-N-DZ 
               
               
                 XPO5 
                 DDX1 
                 6 
                 2 
                 SK-N-DZ 
               
               
                 ZDBF2 
                 DDX1 
                 2 
                 2 
                 SK-N-DZ 
               
               
                 CHCHD3 
                 GNAS 
                 7 
                 20 
                 SK-N-DZ 
               
               
                 HIPK3 
                 GNAS 
                 11 
                 20 
                 SK-N-DZ 
               
               
                 KDM2A 
                 GNAS 
                 11 
                 20 
                 SK-N-DZ 
               
               
                 P4HTM 
                 GNAS 
                 3 
                 20 
                 SK-N-DZ 
               
               
                 PLEKHO2 
                 GNAS 
                 15 
                 20 
                 SK-N-DZ 
               
               
                 SERINC3 
                 GNAS 
                 20 
                 20 
                 SK-N-DZ 
               
               
                 STAG2 
                 GNAS 
                 23 
                 20 
                 SK-N-DZ 
               
               
                 FAM165B 
                 NUP107 
                 21 
                 12 
                 SK-N-DZ 
               
               
                 PHF3 
                 NUP107 
                 6 
                 12 
                 SK-N-DZ 
               
               
                 RAP1B 
                 NUP107 
                 12 
                 12 
                 SK-N-DZ 
               
               
                 SLC35E3 
                 NUP107 
                 12 
                 12 
                 SK-N-DZ 
               
               
                 TCP1 
                 NUP107 
                 6 
                 12 
                 SK-N-DZ 
               
               
                 ADAM10 
                 ANXA2 
                 15 
                 15 
                 SK-N-DZ 
               
               
                 LOC642776 
                 ANXA2 
                 23 
                 15 
                 SK-N-DZ 
               
               
                 NPTN 
                 ANXA2 
                 15 
                 15 
                 SK-N-DZ 
               
               
                 TUBB6 
                 ANXA2 
                 18 
                 15 
                 SK-N-DZ 
               
               
                 YWHAH 
                 ANXA2 
                 22 
                 15 
                 SK-N-DZ 
               
               
                 PROSC 
                 FAM120B 
                 8 
                 6 
                 SK-N-DZ 
               
               
                 ZNF519 
                 FAM120B 
                 18 
                 6 
                 SK-N-DZ 
               
               
                 ARHGAP39 
                 FAM156B 
                 8 
                 23 
                 SK-N-DZ 
               
               
                 EXD3 
                 FAM156B 
                 9 
                 23 
                 SK-N-DZ 
               
               
                 KANK2 
                 FAM156B 
                 19 
                 23 
                 SK-N-DZ 
               
               
                 TGM2 
                 FAM156B 
                 20 
                 23 
                 SK-N-DZ 
               
               
                 ANAPC16 
                 GNAS 
                 10 
                 20 
                 SK-N-DZ 
               
               
                 APBB2 
                 GNAS 
                 4 
                 20 
                 SK-N-DZ 
               
               
                 ARHGEF10 
                 GNAS 
                 8 
                 20 
                 SK-N-DZ 
               
               
                 ASAP1 
                 GNAS 
                 8 
                 20 
                 SK-N-DZ 
               
               
                 BRCA1P1 
                 GNAS 
                 17 
                 20 
                 SK-N-DZ 
               
               
                 CCAR1 
                 GNAS 
                 10 
                 20 
                 SK-N-DZ 
               
               
                 CCDC101 
                 GNAS 
                 16 
                 20 
                 SK-N-DZ 
               
               
                 FAM119B 
                 GNAS 
                 12 
                 20 
                 SK-N-DZ 
               
               
                 ITCH 
                 GNAS 
                 20 
                 20 
                 SK-N-DZ 
               
               
                 NAP1L1 
                 GNAS 
                 12 
                 20 
                 SK-N-DZ 
               
               
                 RBM14 
                 GNAS 
                 11 
                 20 
                 SK-N-DZ 
               
               
                 RPL31 
                 GNAS 
                 2 
                 20 
                 SK-N-DZ 
               
               
                 SFRS18 
                 GNAS 
                 6 
                 20 
                 SK-N-DZ 
               
               
                 TCF4 
                 GNAS 
                 18 
                 20 
                 SK-N-DZ 
               
               
                 TRAF3 
                 GNAS 
                 14 
                 20 
                 SK-N-DZ 
               
               
                 VAPB 
                 GNAS 
                 20 
                 20 
                 SK-N-DZ 
               
               
                 ZMYND8 
                 GNAS 
                 20 
                 20 
                 SK-N-DZ 
               
               
                 C7orf50 
                 SUN1 
                 7 
                 7 
                 SK-N-DZ 
               
               
                 HEATR2 
                 SUN1 
                 7 
                 7 
                 SK-N-DZ 
               
               
                 MAD1L1 
                 SUN1 
                 7 
                 7 
                 SK-N-DZ 
               
               
                 PRKAR1B 
                 SUN1 
                 7 
                 7 
                 SK-N-DZ 
               
               
                 PRKAR1B 
                 SUN1 
                 7 
                 7 
                 SK-N-DZ 
               
               
                 TRA2A 
                 SUN1 
                 7 
                 7 
                 SK-N-DZ 
               
               
                   
               
             
          
         
       
     
         [0136]    Table 9 shows the lists of 5′ networks of fusion transcripts. 
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 9 
               
             
             
               
                   
               
               
                 Identification of 5′ natural networks of the fusion 
               
               
                 transcripts in different cancer cell lines. Gene names 
               
               
                 have been abbreviated to reduce space. If the complex 
               
               
                 gene names adopted by NCBI&#39;s Aceview contain two more 
               
               
                 names connected by “and”, we have used the first 
               
               
                 gene name as Gene IDs. 
               
               
                 The 5′ natural networks formed by fusion transcripts. 
               
             
          
           
               
                 5′ Genes 
                 3′ Genes 
                 5′ Chr 
                 3′ Chr 
                 Cancer Cells 
               
               
                   
               
             
          
           
               
                 ABCC3 
                 KRT8 
                 17 
                 12 
                 A549 
               
               
                 ABCC3 
                 SDCCAG3 
                 17 
                 9 
                 A549 
               
               
                 ABCC3 
                 2-Sep 
                 17 
                 2 
                 A549 
               
               
                 ABCC3 
                 TBCD 
                 17 
                 17 
                 A549 
               
               
                 ABCC3 
                 ZNF598 
                 17 
                 16 
                 A549 
               
               
                 ASPH 
                 C9orf3 
                 8 
                 9 
                 A549 
               
               
                 ASPH 
                 C9orf3 
                 8 
                 9 
                 A549 
               
               
                 ASPH 
                 FAM120B 
                 8 
                 6 
                 A549 
               
               
                 ASPH 
                 MTCP1NB 
                 8 
                 23 
                 A549 
               
               
                 ASPH 
                 YLPM1 
                 8 
                 14 
                 A549 
               
               
                 CALM2 
                 ANKMY1 
                 2 
                 2 
                 A549 
               
               
                 CALM2 
                 C9orf3 
                 2 
                 9 
                 A549 
               
               
                 CALM2 
                 CRIM1 
                 2 
                 2 
                 A549 
               
               
                 CALM2 
                 CTBP1 
                 2 
                 4 
                 A549 
               
               
                 CALM2 
                 CTBP1 
                 2 
                 4 
                 A549 
               
               
                 CALM2 
                 GNA11 
                 2 
                 19 
                 A549 
               
               
                 CALM2 
                 MAFK 
                 2 
                 7 
                 A549 
               
               
                 CALM2 
                 SBNO2 
                 2 
                 19 
                 A549 
               
               
                 CALM2 
                 TSPAN4 
                 2 
                 11 
                 A549 
               
               
                 CALM2 
                 TTC7A 
                 2 
                 2 
                 A549 
               
               
                 CALM2 
                 ZDHHC7 
                 2 
                 16 
                 A549 
               
               
                 CPSF4 
                 FSCN1 
                 7 
                 7 
                 A549 
               
               
                 CPSF6 
                 CHMP1A 
                 12 
                 16 
                 A549 
               
               
                 CPSF6 
                 ENY2 
                 12 
                 8 
                 A549 
               
               
                 CPSF6 
                 EZH2 
                 12 
                 7 
                 A549 
               
               
                 CPSF6 
                 HDAC7 
                 12 
                 12 
                 A549 
               
               
                 CPSF6 
                 HNRPDL 
                 12 
                 4 
                 A549 
               
               
                 CPSF6 
                 NUP107 
                 12 
                 12 
                 A549 
               
               
                 CPSF6 
                 PDE4B 
                 12 
                 1 
                 A549 
               
               
                 CPSF6 
                 RAP1B 
                 12 
                 12 
                 A549 
               
               
                 CPSF6 
                 RPL3 
                 12 
                 22 
                 A549 
               
               
                 CPSF6 
                 SPG7 
                 12 
                 16 
                 A549 
               
               
                 CPSF6 
                 TAF1 
                 12 
                 11 
                 A549 
               
               
                 CYP24A1 
                 AKR1E2 
                 20 
                 10 
                 A549 
               
               
                 CYP24A1 
                 C9orf3 
                 20 
                 9 
                 A549 
               
               
                 CYP24A1 
                 CDK12 
                 20 
                 17 
                 A549 
               
               
                 CYP24A1 
                 CDK12 
                 20 
                 17 
                 A549 
               
               
                 CYP24A1 
                 CLDND2 
                 20 
                 19 
                 A549 
               
               
                 CYP24A1 
                 CYHR1 
                 20 
                 8 
                 A549 
               
               
                 CYP24A1 
                 CYHR1 
                 20 
                 8 
                 A549 
               
               
                 CYP24A1 
                 DAP3 
                 20 
                 1 
                 A549 
               
               
                 CYP24A1 
                 DDX5 
                 20 
                 17 
                 A549 
               
               
                 CYP24A1 
                 FNIP1 
                 20 
                 5 
                 A549 
               
               
                 CYP24A1 
                 HEATR2 
                 20 
                 7 
                 A549 
               
               
                 CYP24A1 
                 KAT5 
                 20 
                 11 
                 A549 
               
               
                 CYP24A1 
                 LAPTM4B 
                 20 
                 8 
                 A549 
               
               
                 CYP24A1 
                 LEMD2 
                 20 
                 6 
                 A549 
               
               
                 CYP24A1 
                 LMNB2 
                 20 
                 19 
                 A549 
               
               
                 CYP24A1 
                 LOC100049716 
                 20 
                 12 
                 A549 
               
               
                 CYP24A1 
                 LRP5 
                 20 
                 11 
                 A549 
               
               
                 CYP24A1 
                 OTUD3 
                 20 
                 1 
                 A549 
               
               
                 CYP24A1 
                 PRKCE 
                 20 
                 2 
                 A549 
               
               
                 CYP24A1 
                 PRR13 
                 20 
                 12 
                 A549 
               
               
                 CYP24A1 
                 PRR13 
                 20 
                 12 
                 A549 
               
               
                 CYP24A1 
                 PSMC4 
                 20 
                 19 
                 A549 
               
               
                 CYP24A1 
                 SHARPIN 
                 20 
                 8 
                 A549 
               
               
                 CYP24A1 
                 SLC25A37 
                 20 
                 8 
                 A549 
               
               
                 CYP24A1 
                 SPG7 
                 20 
                 16 
                 A549 
               
               
                 CYP24A1 
                 SPG7 
                 20 
                 16 
                 A549 
               
               
                 CYP24A1 
                 SRSF1 
                 20 
                 17 
                 A549 
               
               
                 CYP24A1 
                 STT3A 
                 20 
                 11 
                 A549 
               
               
                 CYP24A1 
                 TCFL5 
                 20 
                 20 
                 A549 
               
               
                 CYP24A1 
                 TRIO 
                 20 
                 5 
                 A549 
               
               
                 CYP24A1 
                 WDR4 
                 20 
                 21 
                 A549 
               
               
                 CYP24A1 
                 WWP2 
                 20 
                 16 
                 A549 
               
               
                 EEF1D 
                 ARID1A 
                 8 
                 1 
                 A549 
               
               
                 EEF1D 
                 C19orf22 
                 8 
                 19 
                 A549 
               
               
                 EEF1D 
                 C8orf55 
                 8 
                 8 
                 A549 
               
               
                 EEF1D 
                 C9orf3 
                 8 
                 9 
                 A549 
               
               
                 EEF1D 
                 CFL1 
                 8 
                 11 
                 A549 
               
               
                 EEF1D 
                 GTF3C2 
                 8 
                 2 
                 A549 
               
               
                 EEF1D 
                 HDAC4 
                 8 
                 2 
                 A549 
               
               
                 EEF1D 
                 LZTS2 
                 8 
                 10 
                 A549 
               
               
                 EEF1D 
                 MCOLN1 
                 8 
                 19 
                 A549 
               
               
                 EEF1D 
                 NME4 
                 8 
                 16 
                 A549 
               
               
                 EEF1D 
                 TSPAN4 
                 8 
                 11 
                 A549 
               
               
                 EEF1D 
                 TSSC1 
                 8 
                 2 
                 A549 
               
               
                 EEF1D 
                 ZC3H3 
                 8 
                 8 
                 A549 
               
               
                 EEF1D 
                 ZC3H3 
                 8 
                 8 
                 A549 
               
               
                 EEF1D 
                 ZC3H3 
                 8 
                 8 
                 A549 
               
               
                 EEF1D 
                 ZNF598 
                 8 
                 16 
                 A549 
               
               
                 MAD1L1 
                 CARKD 
                 7 
                 13 
                 A549 
               
               
                 MAD1L1 
                 EIF3B 
                 7 
                 7 
                 A549 
               
               
                 MAD1L1 
                 FAM20C 
                 7 
                 7 
                 A549 
               
               
                 MAD1L1 
                 MAFK 
                 7 
                 7 
                 A549 
               
               
                 MAD1L1 
                 MAFK 
                 7 
                 7 
                 A549 
               
               
                 MAD1L1 
                 MAFK 
                 7 
                 7 
                 A549 
               
               
                 ncRNA00188 
                 ALDH1A1 
                 17 
                 9 
                 A549 
               
               
                 ncRNA00188 
                 CKAP5 
                 17 
                 11 
                 A549 
               
               
                 ncRNA00188 
                 OVOL2 
                 17 
                 20 
                 A549 
               
               
                 ncRNA00188 
                 PCSK5 
                 17 
                 9 
                 A549 
               
               
                 ncRNA00188 
                 UBB 
                 17 
                 17 
                 A549 
               
               
                 ncRNA00188 
                 WHSC1 
                 17 
                 4 
                 A549 
               
               
                 PLEC 
                 ANKLE2 
                 8 
                 12 
                 A549 
               
               
                 PLEC 
                 EEF1D 
                 8 
                 8 
                 A549 
               
               
                 PLEC 
                 EEF1D 
                 8 
                 8 
                 A549 
               
               
                 PLEC 
                 HEATR7A 
                 8 
                 8 
                 A549 
               
               
                 PLEC 
                 HEATR7A 
                 8 
                 8 
                 A549 
               
               
                 PLEC 
                 KLHDC2 
                 8 
                 14 
                 A549 
               
               
                 PLEC 
                 NAT8L 
                 8 
                 4 
                 A549 
               
               
                 PLEC 
                 NUDT14 
                 8 
                 14 
                 A549 
               
               
                 PLEC 
                 RNF126 
                 8 
                 19 
                 A549 
               
               
                 PLEC 
                 SDC1 
                 8 
                 2 
                 A549 
               
               
                 PLEC 
                 SHARPIN 
                 8 
                 8 
                 A549 
               
               
                 PLEC 
                 SHARPIN 
                 8 
                 8 
                 A549 
               
               
                 PLEC 
                 TPP1 
                 8 
                 11 
                 A549 
               
               
                 PPP1R12C 
                 ALDOA 
                 19 
                 16 
                 A549 
               
               
                 PPP1R12C 
                 ASPSCR1 
                 19 
                 17 
                 A549 
               
               
                 PPP1R12C 
                 CNN2 
                 19 
                 19 
                 A549 
               
               
                 PPP1R12C 
                 FOSL1 
                 19 
                 11 
                 A549 
               
               
                 PPP1R12C 
                 TSPAN4 
                 19 
                 11 
                 A549 
               
               
                 SNHG3 
                 ATP6V1G2 
                 1 
                 6 
                 A549 
               
               
                 SNHG3 
                 CUL3 
                 1 
                 2 
                 A549 
               
               
                 SNHG3 
                 DHRS3 
                 1 
                 1 
                 A549 
               
               
                 SNHG3 
                 FEN1 
                 1 
                 11 
                 A549 
               
               
                 SNHG3 
                 FLNB 
                 1 
                 3 
                 A549 
               
               
                 SNHG3 
                 HSP90AA1 
                 1 
                 14 
                 A549 
               
               
                 SNHG3 
                 7-Mar 
                 1 
                 2 
                 A549 
               
               
                 SNHG3 
                 NUP107 
                 1 
                 12 
                 A549 
               
               
                 SNHG3 
                 PHACTR4 
                 1 
                 1 
                 A549 
               
               
                 SNHG3 
                 PHACTR4 
                 1 
                 1 
                 A549 
               
               
                 SNHG3 
                 PTCD3 
                 1 
                 2 
                 A549 
               
               
                 SNHG3 
                 SHPK 
                 1 
                 17 
                 A549 
               
               
                 SNHG3 
                 STK3 
                 1 
                 8 
                 A549 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 A549 
               
               
                 SNHG3 
                 XPO1 
                 1 
                 2 
                 A549 
               
               
                 SNHG3 
                 ZNF638 
                 1 
                 2 
                 A549 
               
               
                 SNHG3 
                 ABCE1 
                 1 
                 4 
                 CUTLL 
               
               
                 SNHG3 
                 CTCF 
                 1 
                 16 
                 CUTLL 
               
               
                 SNHG3 
                 GIGYF2 
                 1 
                 2 
                 CUTLL 
               
               
                 SNHG3 
                 NFS1 
                 1 
                 20 
                 CUTLL 
               
               
                 SNHG3 
                 PDXDC1 
                 1 
                 16 
                 CUTLL 
               
               
                 SNHG3 
                 PKM2 
                 1 
                 15 
                 CUTLL 
               
               
                 SNHG3 
                 POLE2 
                 1 
                 14 
                 CUTLL 
               
               
                 SNHG3 
                 AKR1A1 
                 1 
                 1 
                 H460 
               
               
                 SNHG3 
                 DAP3 
                 1 
                 1 
                 H460 
               
               
                 SNHG3 
                 FDPS 
                 1 
                 1 
                 H460 
               
               
                 SNHG3 
                 PRR13 
                 1 
                 12 
                 H460 
               
               
                 SNHG3 
                 PSMD3 
                 1 
                 17 
                 H460 
               
               
                 SNHG3 
                 RPF2 
                 1 
                 6 
                 H460 
               
               
                 SNHG3 
                 RRP36 
                 1 
                 6 
                 H460 
               
               
                 SNHG3 
                 SETX 
                 1 
                 9 
                 H460 
               
               
                 SNHG3 
                 SMARCAD1 
                 1 
                 4 
                 H460 
               
               
                 SNHG3 
                 VASP 
                 1 
                 19 
                 H460 
               
               
                 SNHG3 
                 CCT3 
                 1 
                 1 
                 HCT116 
               
               
                 SNHG3 
                 CSNK1A1 
                 1 
                 5 
                 HCT116 
               
               
                 SNHG3 
                 GNB1 
                 1 
                 1 
                 HCT116 
               
               
                 SNHG3 
                 HAUS1 
                 1 
                 18 
                 HCT116 
               
               
                 SNHG3 
                 HSPE1 
                 1 
                 2 
                 HCT116 
               
               
                 SNHG3 
                 MIIP 
                 1 
                 1 
                 HCT116 
               
               
                 SNHG3 
                 NFYB 
                 1 
                 12 
                 HCT116 
               
               
                 SNHG3 
                 PDXDC1 
                 1 
                 16 
                 HCT116 
               
               
                 SNHG3 
                 PSMG3 
                 1 
                 7 
                 HCT116 
               
               
                 SNHG3 
                 RPLP0 
                 1 
                 12 
                 HCT116 
               
               
                 SNHG3 
                 SERINC2 
                 1 
                 1 
                 HCT116 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 HCT116 
               
               
                 SNHG3 
                 ANXA2 
                 1 
                 15 
                 Hela-3 
               
               
                 SNHG3 
                 DDX17 
                 1 
                 22 
                 Hela-3 
               
               
                 SNHG3 
                 ENO1 
                 1 
                 1 
                 Hela-3 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 Hela-3 
               
               
                 SNHG3 
                 FIP1L1 
                 1 
                 4 
                 Hela-3 
               
               
                 SNHG3 
                 GDI2 
                 1 
                 10 
                 Hela-3 
               
               
                 SNHG3 
                 GIGYF2 
                 1 
                 2 
                 Hela-3 
               
               
                 SNHG3 
                 GNAS 
                 1 
                 20 
                 Hela-3 
               
               
                 SNHG3 
                 INCENP 
                 1 
                 11 
                 Hela-3 
               
               
                 SNHG3 
                 ITGB3BP 
                 1 
                 1 
                 Hela-3 
               
               
                 SNHG3 
                 NDUFS1 
                 1 
                 2 
                 Hela-3 
               
               
                 SNHG3 
                 PFKP 
                 1 
                 10 
                 Hela-3 
               
               
                 SNHG3 
                 PKM2 
                 1 
                 15 
                 Hela-3 
               
               
                 SNHG3 
                 PRMT5 
                 1 
                 14 
                 Hela-3 
               
               
                 SNHG3 
                 RFWD2 
                 1 
                 1 
                 Hela-3 
               
               
                 SNHG3 
                 SENP3 
                 1 
                 17 
                 Hela-3 
               
               
                 SNHG3 
                 SNHG12 
                 1 
                 1 
                 Hela-3 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 Hela-3 
               
               
                 SNHG3 
                 UBR5 
                 1 
                 8 
                 Hela-3 
               
               
                 SNHG4 
                 ANKLE2 
                 5 
                 12 
                 Hela-3 
               
               
                 SNHG4 
                 CLCN7 
                 5 
                 16 
                 Hela-3 
               
               
                 SNHG4 
                 KIAA0368 
                 5 
                 9 
                 Hela-3 
               
               
                 SNHG4 
                 MBD2 
                 5 
                 18 
                 Hela-3 
               
               
                 SNHG4 
                 UBE2D2 
                 5 
                 5 
                 Hela-3 
               
               
                 EEF1D 
                 GNAS 
                 8 
                 20 
                 HepG2 
               
               
                 EEF1D 
                 MAD1L1 
                 8 
                 7 
                 HepG2 
               
               
                 EEF1D 
                 PTPRN2 
                 8 
                 7 
                 HepG2 
               
               
                 EEF1D 
                 SHC2 
                 8 
                 19 
                 HepG2 
               
               
                 EEF1D 
                 TSPAN4 
                 8 
                 11 
                 HepG2 
               
               
                 EEF1D 
                 TSTA3 
                 8 
                 8 
                 HepG2 
               
               
                 ELL2 
                 CAST 
                 5 
                 5 
                 HepG2 
               
               
                 ELL2 
                 CAST 
                 5 
                 5 
                 HepG2 
               
               
                 ELL2 
                 PFDN1 
                 5 
                 5 
                 HepG2 
               
               
                 ELL2 
                 PFDN1 
                 5 
                 5 
                 HepG2 
               
               
                 ELL2 
                 RHOBTB3 
                 5 
                 5 
                 HepG2 
               
               
                 HECTD1 
                 AFP 
                 14 
                 4 
                 HepG2 
               
               
                 HECTD1 
                 ARHGAP5 
                 14 
                 14 
                 HepG2 
               
               
                 HECTD1 
                 C14orf126 
                 14 
                 14 
                 HepG2 
               
               
                 HECTD1 
                 C14orf126 
                 14 
                 14 
                 HepG2 
               
               
                 HECTD1 
                 PVRL3 
                 14 
                 3 
                 HepG2 
               
               
                 HECTD1 
                 STRN3 
                 14 
                 14 
                 HepG2 
               
               
                 HNRNPH1 
                 CTTN 
                 5 
                 11 
                 HepG2 
               
               
                 HNRNPH1 
                 DDB1 
                 5 
                 11 
                 HepG2 
               
               
                 HNRNPH1 
                 FN1 
                 5 
                 2 
                 HepG2 
               
               
                 HNRNPH1 
                 GNAS 
                 5 
                 20 
                 HepG2 
               
               
                 HNRNPH1 
                 IGF1R 
                 5 
                 15 
                 HepG2 
               
               
                 HNRNPH1 
                 SQSTM1 
                 5 
                 5 
                 HepG2 
               
               
                 LOC375010 
                 C14orf126 
                 1 
                 14 
                 HepG2 
               
               
                 LOC375010 
                 C14orf126 
                 1 
                 14 
                 HepG2 
               
               
                 LOC375010 
                 CSE1L 
                 1 
                 20 
                 HepG2 
               
               
                 LOC375010 
                 CSE1L 
                 1 
                 20 
                 HepG2 
               
               
                 LOC375010 
                 EEF1E1 
                 1 
                 6 
                 HepG2 
               
               
                 LOC375010 
                 EEF1E1 
                 1 
                 6 
                 HepG2 
               
               
                 LOC375010 
                 GOLGA8B 
                 1 
                 15 
                 HepG2 
               
               
                 LOC375010 
                 HNRNPC 
                 1 
                 14 
                 HepG2 
               
               
                 LOC375010 
                 KIAA0146 
                 1 
                 8 
                 HepG2 
               
               
                 LOC375010 
                 KIAA0146 
                 1 
                 8 
                 HepG2 
               
               
                 LOC375010 
                 PIK3C3 
                 1 
                 18 
                 HepG2 
               
               
                 LOC375010 
                 SEC23A 
                 1 
                 14 
                 HepG2 
               
               
                 LOC375010 
                 SP140L 
                 1 
                 2 
                 HepG2 
               
               
                 LOC375010 
                 ZFR 
                 1 
                 5 
                 HepG2 
               
               
                 ncRNA00188 
                 ANXA2 
                 17 
                 15 
                 HepG2 
               
               
                 ncRNA00188 
                 ATR 
                 17 
                 3 
                 HepG2 
               
               
                 ncRNA00188 
                 C19orf48 
                 17 
                 19 
                 HepG2 
               
               
                 ncRNA00188 
                 CTNNBL1 
                 17 
                 20 
                 HepG2 
               
               
                 ncRNA00188 
                 MRPL3 
                 17 
                 3 
                 HepG2 
               
               
                 ncRNA00188 
                 SND1 
                 17 
                 7 
                 HepG2 
               
               
                 ncRNA00188 
                 SNHG7 
                 17 
                 9 
                 HepG2 
               
               
                 ncRNA00188 
                 TPI1 
                 17 
                 12 
                 HepG2 
               
               
                 ncRNA00188 
                 UBAP2 
                 17 
                 9 
                 HepG2 
               
               
                 ncRNA00188 
                 WIPF2 
                 17 
                 17 
                 HepG2 
               
               
                 SNHG3 
                 AHSG 
                 1 
                 3 
                 HepG2 
               
               
                 SNHG3 
                 AHSG 
                 1 
                 3 
                 HepG2 
               
               
                 SNHG3 
                 ANKRD17 
                 1 
                 4 
                 HepG2 
               
               
                 SNHG3 
                 ATG9A 
                 1 
                 2 
                 HepG2 
               
               
                 SNHG3 
                 ATP5B 
                 1 
                 12 
                 HepG2 
               
               
                 SNHG3 
                 CCNT1 
                 1 
                 12 
                 HepG2 
               
               
                 SNHG3 
                 CDHR2 
                 1 
                 5 
                 HepG2 
               
               
                 SNHG3 
                 CSE1L 
                 1 
                 20 
                 HepG2 
               
               
                 SNHG3 
                 DHRS3 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 DYNC1H1 
                 1 
                 14 
                 HepG2 
               
               
                 SNHG3 
                 EEF1D 
                 1 
                 8 
                 HepG2 
               
               
                 SNHG3 
                 EIF3E 
                 1 
                 8 
                 HepG2 
               
               
                 SNHG3 
                 ENO1 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 FARP1 
                 1 
                 13 
                 HepG2 
               
               
                 SNHG3 
                 FN1 
                 1 
                 2 
                 HepG2 
               
               
                 SNHG3 
                 FN1 
                 1 
                 2 
                 HepG2 
               
               
                 SNHG3 
                 GFPT1 
                 1 
                 2 
                 HepG2 
               
               
                 SNHG3 
                 GTF2IRD1 
                 1 
                 7 
                 HepG2 
               
               
                 SNHG3 
                 HAUS1 
                 1 
                 18 
                 HepG2 
               
               
                 SNHG3 
                 HNRNPC 
                 1 
                 14 
                 HepG2 
               
               
                 SNHG3 
                 IMP3 
                 1 
                 15 
                 HepG2 
               
               
                 SNHG3 
                 KIF1B 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 KIF2A 
                 1 
                 5 
                 HepG2 
               
               
                 SNHG3 
                 LDHA 
                 1 
                 11 
                 HepG2 
               
               
                 SNHG3 
                 LSM2 
                 1 
                 6 
                 HepG2 
               
               
                 SNHG3 
                 NFS1 
                 1 
                 20 
                 HepG2 
               
               
                 SNHG3 
                 NPL 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 PPA1 
                 1 
                 10 
                 HepG2 
               
               
                 SNHG3 
                 PRR13 
                 1 
                 12 
                 HepG2 
               
               
                 SNHG3 
                 PSMB2 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 PSMD3 
                 1 
                 17 
                 HepG2 
               
               
                 SNHG3 
                 PUS7 
                 1 
                 7 
                 HepG2 
               
               
                 SNHG3 
                 RBM39 
                 1 
                 20 
                 HepG2 
               
               
                 SNHG3 
                 RPL17 
                 1 
                 18 
                 HepG2 
               
               
                 SNHG3 
                 RPL18A 
                 1 
                 19 
                 HepG2 
               
               
                 SNHG3 
                 SEC24B 
                 1 
                 4 
                 HepG2 
               
               
                 SNHG3 
                 SENP3 
                 1 
                 17 
                 HepG2 
               
               
                 SNHG3 
                 SNRPN 
                 1 
                 15 
                 HepG2 
               
               
                 SNHG3 
                 SPNS1 
                 1 
                 16 
                 HepG2 
               
               
                 SNHG3 
                 SRSF1 
                 1 
                 17 
                 HepG2 
               
               
                 SNHG3 
                 SUN1 
                 1 
                 7 
                 HepG2 
               
               
                 SNHG3 
                 TAF12 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 TAF12 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 TBCA 
                 1 
                 5 
                 HepG2 
               
               
                 SNHG3 
                 TCF25 
                 1 
                 16 
                 HepG2 
               
               
                 SNHG3 
                 TLK1 
                 1 
                 2 
                 HepG2 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 TRNP1 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 UIMC1 
                 1 
                 5 
                 HepG2 
               
               
                 SNHG3 
                 USP48 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 ZFYVE16 
                 1 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 CTNNA1 
                 5 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 ETF1 
                 5 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 GTF2I 
                 5 
                 7 
                 HepG2 
               
               
                 SNHG4 
                 HP1BP3 
                 5 
                 1 
                 HepG2 
               
               
                 SNHG4 
                 PAIP2 
                 5 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 RHOA 
                 5 
                 3 
                 HepG2 
               
               
                 SNHG4 
                 ROCK2 
                 5 
                 2 
                 HepG2 
               
               
                 SNHG4 
                 SIL1 
                 5 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 EIF4G3 
                 5 
                 1 
                 HT1080 
               
               
                 SNHG4 
                 GLYR1 
                 5 
                 16 
                 HT1080 
               
               
                 SNHG4 
                 NVL 
                 5 
                 1 
                 HT1080 
               
               
                 SNHG4 
                 PHF14 
                 5 
                 7 
                 HT1080 
               
               
                 SNHG4 
                 RTN3 
                 5 
                 11 
                 HT1080 
               
               
                 SNHG4 
                 UCHL5 
                 5 
                 1 
                 HT1080 
               
               
                 ACADM 
                 AP1G1 
                 1 
                 16 
                 K562 
               
               
                 ACADM 
                 AP1G1 
                 1 
                 16 
                 K562 
               
               
                 ACADM 
                 C6orf191 
                 1 
                 6 
                 K562 
               
               
                 ACADM 
                 MSH4 
                 1 
                 1 
                 K562 
               
               
                 ACADM 
                 NPL 
                 1 
                 1 
                 K562 
               
               
                 ACADM 
                 NPL 
                 1 
                 1 
                 K562 
               
               
                 ACADM 
                 VCL 
                 1 
                 10 
                 K562 
               
               
                 ACADM 
                 VCL 
                 1 
                 10 
                 K562 
               
               
                 C7orf44 
                 BLVRA 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 PSMA2 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 PSMA2 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 TAX1BP1 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 TAX1BP1 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 URGCP 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 WIPI2 
                 7 
                 7 
                 K562 
               
               
                 C7orf58 
                 GOSR2 
                 7 
                 17 
                 K562 
               
               
                 C7orf58 
                 NMU 
                 7 
                 4 
                 K562 
               
               
                 C7orf58 
                 RPL13 
                 7 
                 16 
                 K562 
               
               
                 C7orf58 
                 TUBGCP6 
                 7 
                 22 
                 K562 
               
               
                 C7orf58 
                 UBAP2L 
                 7 
                 1 
                 K562 
               
               
                 SNHG3 
                 RPL17 
                 1 
                 18 
                 HepG2 
               
               
                 SNHG3 
                 RPL18A 
                 1 
                 19 
                 HepG2 
               
               
                 SNHG3 
                 SEC24B 
                 1 
                 4 
                 HepG2 
               
               
                 SNHG3 
                 SENP3 
                 1 
                 17 
                 HepG2 
               
               
                 SNHG3 
                 SNRPN 
                 1 
                 15 
                 HepG2 
               
               
                 SNHG3 
                 SPNS1 
                 1 
                 16 
                 HepG2 
               
               
                 SNHG3 
                 SRSF1 
                 1 
                 17 
                 HepG2 
               
               
                 SNHG3 
                 SUN1 
                 1 
                 7 
                 HepG2 
               
               
                 SNHG3 
                 TAF12 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 TAF12 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 TBCA 
                 1 
                 5 
                 HepG2 
               
               
                 SNHG3 
                 TCF25 
                 1 
                 16 
                 HepG2 
               
               
                 SNHG3 
                 TLK1 
                 1 
                 2 
                 HepG2 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 TRNP1 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 UIMC1 
                 1 
                 5 
                 HepG2 
               
               
                 SNHG3 
                 USP48 
                 1 
                 1 
                 HepG2 
               
               
                 SNHG3 
                 ZFYVE16 
                 1 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 CTNNA1 
                 5 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 ETF1 
                 5 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 GTF2I 
                 5 
                 7 
                 HepG2 
               
               
                 SNHG4 
                 HP1BP3 
                 5 
                 1 
                 HepG2 
               
               
                 SNHG4 
                 PAIP2 
                 5 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 RHOA 
                 5 
                 3 
                 HepG2 
               
               
                 SNHG4 
                 ROCK2 
                 5 
                 2 
                 HepG2 
               
               
                 SNHG4 
                 SIL1 
                 5 
                 5 
                 HepG2 
               
               
                 SNHG4 
                 EIF4G3 
                 5 
                 1 
                 HT1080 
               
               
                 SNHG4 
                 GLYR1 
                 5 
                 16 
                 HT1080 
               
               
                 SNHG4 
                 NVL 
                 5 
                 1 
                 HT1080 
               
               
                 SNHG4 
                 PHF14 
                 5 
                 7 
                 HT1080 
               
               
                 SNHG4 
                 RTN3 
                 5 
                 11 
                 HT1080 
               
               
                 SNHG4 
                 UCHL5 
                 5 
                 1 
                 HT1080 
               
               
                 ACADM 
                 AP1G1 
                 1 
                 16 
                 K562 
               
               
                 ACADM 
                 AP1G1 
                 1 
                 16 
                 K562 
               
               
                 ACADM 
                 C6orf191 
                 1 
                 6 
                 K562 
               
               
                 ACADM 
                 MSH4 
                 1 
                 1 
                 K562 
               
               
                 ACADM 
                 NPL 
                 1 
                 1 
                 K562 
               
               
                 ACADM 
                 NPL 
                 1 
                 1 
                 K562 
               
               
                 ACADM 
                 VCL 
                 1 
                 10 
                 K562 
               
               
                 ACADM 
                 VCL 
                 1 
                 10 
                 K562 
               
               
                 C7orf44 
                 BLVRA 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 PSMA2 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 PSMA2 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 TAX1BP1 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 TAX1BP1 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 URGCP 
                 7 
                 7 
                 K562 
               
               
                 C7orf44 
                 WIPI2 
                 7 
                 7 
                 K562 
               
               
                 C7orf58 
                 GOSR2 
                 7 
                 17 
                 K562 
               
               
                 C7orf58 
                 NMU 
                 7 
                 4 
                 K562 
               
               
                 C7orf58 
                 RPL13 
                 7 
                 16 
                 K562 
               
               
                 C7orf58 
                 TUBGCP6 
                 7 
                 22 
                 K562 
               
               
                 C7orf58 
                 UBAP2L 
                 7 
                 1 
                 K562 
               
               
                 CCDC26 
                 ASAP1 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 ASAP1 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 ASAP1 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 FAM49B 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 FAM49B 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 FAM49B 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 LOC728724 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 LOC728724 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 LOC728724 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 LOC728724 
                 8 
                 8 
                 K562 
               
               
                 CCDC26 
                 PVT1 
                 8 
                 8 
                 K562 
               
               
                 CHD2 
                 CCNF 
                 15 
                 16 
                 K562 
               
               
                 CHD2 
                 PCF11 
                 15 
                 11 
                 K562 
               
               
                 CHD2 
                 SDF2 
                 15 
                 17 
                 K562 
               
               
                 CHD2 
                 SEPSECS 
                 15 
                 4 
                 K562 
               
               
                 CHD2 
                 SRSF1 
                 15 
                 17 
                 K562 
               
               
                 CPSF6 
                 BTK 
                 12 
                 23 
                 K562 
               
               
                 CPSF6 
                 C6orf203 
                 12 
                 6 
                 K562 
               
               
                 CPSF6 
                 CCT2 
                 12 
                 12 
                 K562 
               
               
                 CPSF6 
                 CSNK1D 
                 12 
                 17 
                 K562 
               
               
                 CPSF6 
                 FAM120AOS 
                 12 
                 9 
                 K562 
               
               
                 CPSF6 
                 GCFC1 
                 12 
                 21 
                 K562 
               
               
                 CPSF6 
                 KIAA0586 
                 12 
                 14 
                 K562 
               
               
                 CPSF6 
                 MRPL44 
                 12 
                 2 
                 K562 
               
               
                 CPSF6 
                 UBE2L3 
                 12 
                 22 
                 K562 
               
               
                 CPSF6 
                 UQCRB 
                 12 
                 8 
                 K562 
               
               
                 CTBP2 
                 ATE1 
                 10 
                 10 
                 K562 
               
               
                 CTBP2 
                 MAEA 
                 10 
                 4 
                 K562 
               
               
                 CTBP2 
                 MAP4 
                 10 
                 3 
                 K562 
               
               
                 CTBP2 
                 METTL10 
                 10 
                 10 
                 K562 
               
               
                 CTBP2 
                 OCIAD1 
                 10 
                 4 
                 K562 
               
               
                 CTBP2 
                 PSMB1 
                 10 
                 6 
                 K562 
               
               
                 CTBP2 
                 ZRANB1 
                 10 
                 10 
                 K562 
               
               
                 EXOC4 
                 CHCHD3 
                 7 
                 7 
                 K562 
               
               
                 EXOC4 
                 CHCHD3 
                 7 
                 7 
                 K562 
               
               
                 EXOC4 
                 CHCHD3 
                 7 
                 7 
                 K562 
               
               
                 EXOC4 
                 CHCHD3 
                 7 
                 7 
                 K562 
               
               
                 EXOC4 
                 SHFM1 
                 7 
                 7 
                 K562 
               
               
                 EXOC4 
                 TMEM209 
                 7 
                 7 
                 K562 
               
               
                 EXOC4 
                 TMEM209 
                 7 
                 7 
                 K562 
               
               
                 EXOC4 
                 UBN2 
                 7 
                 7 
                 K562 
               
               
                 HDLBP 
                 ANKMY1 
                 2 
                 2 
                 K562 
               
               
                 HDLBP 
                 ANKMY1 
                 2 
                 2 
                 K562 
               
               
                 HDLBP 
                 GNAS 
                 2 
                 20 
                 K562 
               
               
                 HDLBP 
                 NDUFA10 
                 2 
                 2 
                 K562 
               
               
                 HDLBP 
                 PASK 
                 2 
                 2 
                 K562 
               
               
                 HDLBP 
                 THAP4 
                 2 
                 2 
                 K562 
               
               
                 HDLBP 
                 TRPC4AP 
                 2 
                 20 
                 K562 
               
               
                 HNRNPH1 
                 CANX 
                 5 
                 5 
                 K562 
               
               
                 HNRNPH1 
                 IARS 
                 5 
                 9 
                 K562 
               
               
                 HNRNPH1 
                 MAML1 
                 5 
                 5 
                 K562 
               
               
                 HNRNPH1 
                 NDC80 
                 5 
                 18 
                 K562 
               
               
                 HNRNPH1 
                 PPIG 
                 5 
                 2 
                 K562 
               
               
                 HNRNPH1 
                 SQSTM1 
                 5 
                 5 
                 K562 
               
               
                 HNRNPH1 
                 TBCD 
                 5 
                 17 
                 K562 
               
               
                 HNRNPH1 
                 TXN 
                 5 
                 9 
                 K562 
               
               
                 KIAA0114 
                 FAF1 
                 4 
                 1 
                 K562 
               
               
                 KIAA0114 
                 FKBP4 
                 4 
                 12 
                 K562 
               
               
                 KIAA0114 
                 GNB1 
                 4 
                 1 
                 K562 
               
               
                 KIAA0114 
                 GNB1 
                 4 
                 1 
                 K562 
               
               
                 KIAA0114 
                 MIB1 
                 4 
                 18 
                 K562 
               
               
                 KIAA0114 
                 NRD1 
                 4 
                 1 
                 K562 
               
               
                 KIAA0114 
                 NRD1 
                 4 
                 1 
                 K562 
               
               
                 KIAA0114 
                 PHF14 
                 4 
                 7 
                 K562 
               
               
                 KIAA0114 
                 PHKB 
                 4 
                 16 
                 K562 
               
               
                 KIAA0114 
                 PHKB 
                 4 
                 16 
                 K562 
               
               
                 KIAA0114 
                 PICALM 
                 4 
                 11 
                 K562 
               
               
                 KIAA0114 
                 PRKCB 
                 4 
                 16 
                 K562 
               
               
                 KIAA0114 
                 PRKCB 
                 4 
                 16 
                 K562 
               
               
                 KIAA0114 
                 RPL10 
                 4 
                 23 
                 K562 
               
               
                 KIAA0114 
                 RPL3 
                 4 
                 22 
                 K562 
               
               
                 KIAA0114 
                 TRAPPC3 
                 4 
                 1 
                 K562 
               
               
                 LOC728323 
                 FAM138E 
                 2 
                 15 
                 K562 
               
               
                 LOC728323 
                 FLJ45340 
                 2 
                 7 
                 K562 
               
               
                 LOC728323 
                 RPL23AP53 
                 2 
                 8 
                 K562 
               
               
                 LOC728323 
                 RPL23AP53 
                 2 
                 8 
                 K562 
               
               
                 LOC728323 
                 RPL23AP79 
                 2 
                 19 
                 K562 
               
               
                 LOC728323 
                 WASH3P 
                 2 
                 15 
                 K562 
               
               
                 MCM3APAS 
                 C21orf56 
                 21 
                 21 
                 K562 
               
               
                 MCM3APAS 
                 C21orf56 
                 21 
                 21 
                 K562 
               
               
                 MCM3APAS 
                 DEPDC1B 
                 21 
                 5 
                 K562 
               
               
                 MCM3APAS 
                 PRPF40A 
                 21 
                 2 
                 K562 
               
               
                 MCM3APAS 
                 PTTG1 
                 21 
                 5 
                 K562 
               
               
                 MIR17HG 
                 FAF1 
                 13 
                 1 
                 K562 
               
               
                 MIR17HG 
                 NUP214 
                 13 
                 9 
                 K562 
               
               
                 MIR17HG 
                 NUP214 
                 13 
                 9 
                 K562 
               
               
                 MIR17HG 
                 PANK2 
                 13 
                 20 
                 K562 
               
               
                 MIR17HG 
                 PAPD4 
                 13 
                 5 
                 K562 
               
               
                 ncRNA00188 
                 ANXA2 
                 17 
                 15 
                 K562 
               
               
                 ncRNA00188 
                 BAZ1B 
                 17 
                 7 
                 K562 
               
               
                 ncRNA00188 
                 CKAP5 
                 17 
                 11 
                 K562 
               
               
                 ncRNA00188 
                 CTNNBL1 
                 17 
                 20 
                 K562 
               
               
                 ncRNA00188 
                 EIF5 
                 17 
                 14 
                 K562 
               
               
                 ncRNA00188 
                 IMMP2L 
                 17 
                 7 
                 K562 
               
               
                 ncRNA00188 
                 MAD1L1 
                 17 
                 7 
                 K562 
               
               
                 ncRNA00188 
                 MAD1L1 
                 17 
                 7 
                 K562 
               
               
                 ncRNA00188 
                 PAIP2 
                 17 
                 5 
                 K562 
               
               
                 ncRNA00188 
                 PHF14 
                 17 
                 7 
                 K562 
               
               
                 ncRNA00188 
                 PHF14 
                 17 
                 7 
                 K562 
               
               
                 ncRNA00188 
                 RPS3 
                 17 
                 11 
                 K562 
               
               
                 ncRNA00188 
                 RPS3 
                 17 
                 11 
                 K562 
               
               
                 ncRNA00188 
                 SENP3 
                 17 
                 17 
                 K562 
               
               
                 ncRNA00188 
                 SND1 
                 17 
                 7 
                 K562 
               
               
                 ncRNA00188 
                 SNHG7 
                 17 
                 9 
                 K562 
               
               
                 ncRNA00188 
                 UBAP2 
                 17 
                 9 
                 K562 
               
               
                 RPL27A 
                 APLP2 
                 11 
                 11 
                 K562 
               
               
                 RPL27A 
                 APLP2 
                 11 
                 11 
                 K562 
               
               
                 RPL27A 
                 BAT2L2 
                 11 
                 1 
                 K562 
               
               
                 RPL27A 
                 BAT2L2 
                 11 
                 1 
                 K562 
               
               
                 RPL27A 
                 CCNT1 
                 11 
                 12 
                 K562 
               
               
                 RPL27A 
                 DDIT4 
                 11 
                 10 
                 K562 
               
               
                 RPL27A 
                 HDLBP 
                 11 
                 2 
                 K562 
               
               
                 RPL27A 
                 NVL 
                 11 
                 1 
                 K562 
               
               
                 RPL27A 
                 PLAA 
                 11 
                 9 
                 K562 
               
               
                 RPL27A 
                 RABGAP1L 
                 11 
                 1 
                 K562 
               
               
                 RPL27A 
                 RABGAP1L 
                 11 
                 1 
                 K562 
               
               
                 RPL27A 
                 RNF149 
                 11 
                 2 
                 K562 
               
               
                 RPL27A 
                 RPL35 
                 11 
                 9 
                 K562 
               
               
                 RPL27A 
                 RPS27A 
                 11 
                 2 
                 K562 
               
               
                 RPL27A 
                 RPS27A 
                 11 
                 2 
                 K562 
               
               
                 RPL27A 
                 RPS3 
                 11 
                 11 
                 K562 
               
               
                 RPL27A 
                 SMC4 
                 11 
                 3 
                 K562 
               
               
                 RPL27A 
                 SMC4 
                 11 
                 3 
                 K562 
               
               
                 RPL27A 
                 SND1 
                 11 
                 7 
                 K562 
               
               
                 RPL27A 
                 SND1 
                 11 
                 7 
                 K562 
               
               
                 RPL27A 
                 SRSF2IP 
                 11 
                 12 
                 K562 
               
               
                 RPL27A 
                 SRSF2IP 
                 11 
                 12 
                 K562 
               
               
                 RPL27A 
                 UBE2D2 
                 11 
                 5 
                 K562 
               
               
                 SNHG3 
                 ABCE1 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 ABHD3 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 ABHD3 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 ADCK2 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 ADCK2 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 AKR1A1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 ALG3 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 ALG3 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 ANKHD1 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 ANP32B 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 ANXA2 
                 1 
                 15 
                 K562 
               
               
                 SNHG3 
                 ARL6IP1 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 ARL6IP1 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 ARL6IP1 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 ATP13A3 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 ATP13A3 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 ATP5A1 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 ATP5A1 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 ATP5B 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 ATP5B 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 ATP6V1G2 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 ATP6V1G2 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 ATP6V1G2 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 ATP6V1G2 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 ATP6V1G2 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 BAIAP2L1 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 BAIAP2L1 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 BLVRB 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 BLVRB 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 C11orf48 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 C11orf48 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 C2orf24 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 C9orf5 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 C9orf5 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 CANX 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 CANX 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 CANX 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 CCAR1 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 CCAR1 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 CCDC132 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 CCDC132 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 CCDC18 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 CCNY 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 CCT3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 CCT3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 CCT5 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 CCT5 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 CCT8 
                 1 
                 21 
                 K562 
               
               
                 SNHG3 
                 CCT8 
                 1 
                 21 
                 K562 
               
               
                 SNHG3 
                 CENPE 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 CENPE 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 CHAF1A 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 CHCHD3 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 CHCHD3 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 CNOT1 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 CNOT1 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 CNOT10 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 CNOT10 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 COPA 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 COPA 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 COX5A 
                 1 
                 15 
                 K562 
               
               
                 SNHG3 
                 COX5A 
                 1 
                 15 
                 K562 
               
               
                 SNHG3 
                 COX5A 
                 1 
                 15 
                 K562 
               
               
                 SNHG3 
                 COX5B 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 CRAMP1L 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 CRAMP1L 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 CSE1L 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 CSE1L 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 CSE1L 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 CTCF 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 CUL2 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 CUL2 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 CUL3 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 CWF19L1 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 CWF19L1 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 CYHR1 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DAP3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DARS 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 DARS 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 DCAF6 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DCAF6 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DCAF6 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DCI 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 DDX17 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 DDX17 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 DHRS3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DHX29 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 DHX29 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 DIP2B 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 DIP2B 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 DKC1 
                 1 
                 23 
                 K562 
               
               
                 SNHG3 
                 DKC1 
                 1 
                 23 
                 K562 
               
               
                 SNHG3 
                 DKC1 
                 1 
                 23 
                 K562 
               
               
                 SNHG3 
                 DKFZP686I15217 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 DKFZP686I15217 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 DNAJC11 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 DNAJC7 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 DNAJC7 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 DYNC1H1 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 EEF1B2 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 EEF1D 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 EEF1D 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 EIF2B1 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 EIF2B1 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 EIF2B3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 EIF2B3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 EIF3E 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 ELP2 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 ELP2 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 ENO1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 ENO1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 EPB41 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 EPB41 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 EPS15 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 ESCO1 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 ESYT2 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 EXOC6 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 EXOC6 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 EXOC6 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FAF1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 FARSB 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 FASTKD1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 FASTKD1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 FN3KRP 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 FTSJD2 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 GABPB2 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 GCFC1 
                 1 
                 21 
                 K562 
               
               
                 SNHG3 
                 GCFC1 
                 1 
                 21 
                 K562 
               
               
                 SNHG3 
                 GDI2 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 GDI2 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 GGPS1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 GGPS1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 GNB1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 GNB2L1 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 GNB2L1 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 GPR98 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 GPR98 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 GPR98 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 GSPT1 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 GTF2IRD1 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 GTF3C6 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 GTF3C6 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 GTPBP4 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 H2AFV 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 H2AFV 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 HBS1L 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 HMGA1 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 HNRNPC 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 HNRNPH1 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 HNRNPH1 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 HNRNPH3 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 HNRNPH3 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 HNRNPH3 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 HSP90AA1 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 HSPC157 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 HSPE1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 HUWE1 
                 1 
                 23 
                 K562 
               
               
                 SNHG3 
                 HUWE1 
                 1 
                 23 
                 K562 
               
               
                 SNHG3 
                 ILF2 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 ILF2 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 ILF2 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 ILF3 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 IMP3 
                 1 
                 15 
                 K562 
               
               
                 SNHG3 
                 KARS 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 KARS 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 KIF1B 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 KIF1B 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 KIF2A 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 KIF2A 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 KLK1 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 KRT222 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 KRT222 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 LARP4 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 LARS 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 LARS 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 LCP1 
                 1 
                 13 
                 K562 
               
               
                 SNHG3 
                 LCP1 
                 1 
                 13 
                 K562 
               
               
                 SNHG3 
                 LOC440944 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 LOC440944 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 LOC641298 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 LOC641298 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 LRRC47 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 LSM2 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 LYN 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 LYN 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 MAPK1 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 MAPK1 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 MAPK1 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 MAPK1 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 MBD2 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 MBD2 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 MCM8 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 MDH2 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 METT10D 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 METT10D 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 MFF 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 MRPL3 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 MTOR 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 MYBL2 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 MYL6B 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 MYL6B 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 NDUFAF4 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 NNT 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 NNT 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 NNT 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 NPL 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 NPL 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 NPL 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 NPL 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 NPM1 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 NPM1 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 NSMCE2 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 NSMCE2 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 NUDCD2 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 NUDCD2 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 NUP107 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 NUP214 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 NUP214 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 ODC1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 ODC1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 ODC1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 OVOL2 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 OVOL2 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 PABPC4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PAK1IP1 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 PAK1IP1 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 PARK7 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PARK7 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PARP4 
                 1 
                 13 
                 K562 
               
               
                 SNHG3 
                 PARP4 
                 1 
                 13 
                 K562 
               
               
                 SNHG3 
                 PDCL2 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 PDS5A 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 PFKP 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 PHACTR4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PHACTR4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PHF14 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 PHF20 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 PHKB 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PKM2 
                 1 
                 15 
                 K562 
               
               
                 SNHG3 
                 PKN1 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 PLEKHA4 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 PLEKHA4 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 POLE 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 POLE 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 POLE2 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 PPA1 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 PPM1B 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 PPM1B 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 PRAME 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 PRAME 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 PRAME 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 PRKCB 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 PRKCB 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 PRKDC 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 PRMT5 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 PRPF3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PRPF6 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 PRPF6 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 PRR13 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 PRR13 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 PSMA1 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PSMA1 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PSMD4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PSMD4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PSMD4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PSMG3 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 PSMG3 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 PTCD3 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 PUS7 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 PUS7 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 QRICH2 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 RANBP1 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 NSMCE2 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 NSMCE2 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 NUDCD2 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 NUDCD2 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 NUP107 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 NUP214 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 NUP214 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 ODC1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 ODC1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 ODC1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 OVOL2 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 OVOL2 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 PABPC4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PAK1IP1 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 PAK1IP1 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 PARK7 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PARK7 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PARP4 
                 1 
                 13 
                 K562 
               
               
                 SNHG3 
                 PARP4 
                 1 
                 13 
                 K562 
               
               
                 SNHG3 
                 PDCL2 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 PDS5A 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 PFKP 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 PHACTR4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PHACTR4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PHF14 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 PHF20 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 PHKB 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PICALM 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PKM2 
                 1 
                 15 
                 K562 
               
               
                 SNHG3 
                 PKN1 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 PLEKHA4 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 PLEKHA4 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 POLE 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 POLE 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 POLE2 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 PPA1 
                 1 
                 10 
                 K562 
               
               
                 SNHG3 
                 PPM1B 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 PPM1B 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 PRAME 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 PRAME 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 PRAME 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 PRKCB 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 PRKCB 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 PRKDC 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 PRMT5 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 PRPF3 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PRPF6 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 PRPF6 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 PRR13 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 PRR13 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 PSMA1 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PSMA1 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 PSMD4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PSMD4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PSMD4 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 PSMG3 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 PSMG3 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 PTCD3 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 PUS7 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 PUS7 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 QRICH2 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 RANBP1 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 RANBP1 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 RBM16 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 RBM16 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 RBM39 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 RBM39 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 RBM39 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 RFWD2 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 RHAG 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 RHAG 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 RHAG 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 RHAG 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 RHEB 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 RHOA 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 RNASEH1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 RNF149 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 RNF149 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 RNF4 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 RNF4 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 RPL17 
                 1 
                 18 
                 K562 
               
               
                 SNHG3 
                 RPL18A 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 RPL22 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 RPL23 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 RPL23 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 RPL23 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 RPL3 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 RPL3 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 RPL30 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 RPL30 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 RPL4 
                 1 
                 15 
                 K562 
               
               
                 SNHG3 
                 RPL4 
                 1 
                 15 
                 K562 
               
               
                 SNHG3 
                 RPL5 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 RPN2 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 RPN2 
                 1 
                 20 
                 K562 
               
               
                 SNHG3 
                 RPS18 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 RPS3 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 RPS3 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 RPS5 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 RPS5 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 RPS6KC1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SAGE1 
                 1 
                 23 
                 K562 
               
               
                 SNHG3 
                 SDHB 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SDHB 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SEC24B 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 SEC24B 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 SENP3 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 SENP3 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 SENP3 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 2-Sep 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 2-Sep 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 SERPINB6 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 SERPINB6 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 SETX 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 SF3B3 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 SF3B3 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 SHPK 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 SIKE1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SIKE1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SKI 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SLC38A10 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 SMARCAD1 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 SMARCC1 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 SMARCC1 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 SMC6 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 SMC6 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 SNHG12 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SNHG12 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SNORD1C 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 SNRPD3 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 SNRPD3 
                 1 
                 22 
                 K562 
               
               
                 SNHG3 
                 SON 
                 1 
                 21 
                 K562 
               
               
                 SNHG3 
                 SON 
                 1 
                 21 
                 K562 
               
               
                 SNHG3 
                 SON 
                 1 
                 21 
                 K562 
               
               
                 SNHG3 
                 SP1 
                 1 
                 12 
                 K562 
               
               
                 SNHG3 
                 SPTA1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SPTA1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SRP54 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 SRP54 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 SRP72 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 SRP72 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 SRSF1 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 SRSF11 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 SRSF11 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 STAG2 
                 1 
                 23 
                 K562 
               
               
                 SNHG3 
                 STAG2 
                 1 
                 23 
                 K562 
               
               
                 SNHG3 
                 STAT5B 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 STAT5B 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 STAT5B 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 STIL 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 STIL 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 STIP1 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 STK3 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 STRBP 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 STRBP 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 STRBP 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 TAF12 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 TAF12 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 TAF12 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 TBCA 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 TBCA 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 TCF25 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 TCP1 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 TCP1 
                 1 
                 6 
                 K562 
               
               
                 SNHG3 
                 TFPI 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 TFPI 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 TOPBP1 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 TOPBP1 
                 1 
                 3 
                 K562 
               
               
                 SNHG3 
                 TRAP1 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 TRAP1 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 TRIM33 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 TRIM33 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 TSR1 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 TTC17 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 TTC17 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 TYW1 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 U2AF1 
                 1 
                 21 
                 K562 
               
               
                 SNHG3 
                 U2AF1 
                 1 
                 21 
                 K562 
               
               
                 SNHG3 
                 UAP1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 UAP1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 UBAP2 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 UBAP2 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 UBAP2 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 UBAP2 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 UBB 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 UBE2I 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 UBE2I 
                 1 
                 16 
                 K562 
               
               
                 SNHG3 
                 UBE3C 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 UBE3C 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 UBR5 
                 1 
                 8 
                 K562 
               
               
                 SNHG3 
                 UCHL5 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 UCHL5 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 UIMC1 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 USP48 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 UTP6 
                 1 
                 17 
                 K562 
               
               
                 SNHG3 
                 WDHD1 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 WDHD1 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 WDR43 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 WDR43 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 WHSC1 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 WHSC1 
                 1 
                 4 
                 K562 
               
               
                 SNHG3 
                 XPO1 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 YLPM1 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 YLPM1 
                 1 
                 14 
                 K562 
               
               
                 SNHG3 
                 YY1AP1 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 ZBED5 
                 1 
                 11 
                 K562 
               
               
                 SNHG3 
                 ZBTB8OS 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 ZBTB8OS 
                 1 
                 1 
                 K562 
               
               
                 SNHG3 
                 ZCCHC7 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 ZCCHC7 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 ZCCHC7 
                 1 
                 9 
                 K562 
               
               
                 SNHG3 
                 ZFR 
                 1 
                 5 
                 K562 
               
               
                 SNHG3 
                 ZNF431 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 ZNF431 
                 1 
                 19 
                 K562 
               
               
                 SNHG3 
                 ZNF638 
                 1 
                 2 
                 K562 
               
               
                 SNHG3 
                 ZNF713 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 ZNF713 
                 1 
                 7 
                 K562 
               
               
                 SNHG3 
                 ZNF713 
                 1 
                 7 
                 K562 
               
               
                 SNHG4 
                 AGPS 
                 5 
                 2 
                 K562 
               
               
                 SNHG4 
                 AGPS 
                 5 
                 2 
                 K562 
               
               
                 SNHG4 
                 ATXN2 
                 5 
                 12 
                 K562 
               
               
                 SNHG4 
                 GNAS 
                 5 
                 20 
                 K562 
               
               
                 SNHG4 
                 GTF2I 
                 5 
                 7 
                 K562 
               
               
                 SNHG4 
                 NS3BP 
                 5 
                 11 
                 K562 
               
               
                 SNHG4 
                 NS3BP 
                 5 
                 11 
                 K562 
               
               
                 SNHG4 
                 PICALM 
                 5 
                 11 
                 K562 
               
               
                 SNHG4 
                 PICALM 
                 5 
                 11 
                 K562 
               
               
                 SNHG4 
                 PSMD1 
                 5 
                 2 
                 K562 
               
               
                 SNHG4 
                 RPS27A 
                 5 
                 2 
                 K562 
               
               
                 SNHG4 
                 RPS27A 
                 5 
                 2 
                 K562 
               
               
                 SNHG4 
                 RRN3P3 
                 5 
                 16 
                 K562 
               
               
                 SNHG4 
                 SKP1 
                 5 
                 5 
                 K562 
               
               
                 SNHG4 
                 TMEM66 
                 5 
                 8 
                 K562 
               
               
                 SNHG4 
                 UBE2K 
                 5 
                 4 
                 K562 
               
               
                 SNHG4 
                 UBE2K 
                 5 
                 4 
                 K562 
               
               
                 SNHG4 
                 UBE4B 
                 5 
                 1 
                 K562 
               
               
                 SNHG4 
                 UBE4B 
                 5 
                 1 
                 K562 
               
               
                 SUSD1 
                 HSDL2 
                 9 
                 9 
                 K562 
               
               
                 SUSD1 
                 HSDL2 
                 9 
                 9 
                 K562 
               
               
                 SUSD1 
                 HSDL2 
                 9 
                 9 
                 K562 
               
               
                 SUSD1 
                 KIAA0368 
                 9 
                 9 
                 K562 
               
               
                 SUSD1 
                 KIAA0368 
                 9 
                 9 
                 K562 
               
               
                 SUSD1 
                 ROD1 
                 9 
                 9 
                 K562 
               
               
                 SUSD1 
                 ROD1 
                 9 
                 9 
                 K562 
               
               
                 TAF1 
                 HP1BP3 
                 11 
                 1 
                 K562 
               
               
                 TAF1 
                 HP1BP3 
                 11 
                 1 
                 K562 
               
               
                 TAF1 
                 PICALM 
                 11 
                 11 
                 K562 
               
               
                 TAF1 
                 PICALM 
                 11 
                 11 
                 K562 
               
               
                 TAF1 
                 PRPSAP2 
                 11 
                 17 
                 K562 
               
               
                 TAF1 
                 PSMA1 
                 11 
                 11 
                 K562 
               
               
                 TAF1 
                 PSMA1 
                 11 
                 11 
                 K562 
               
               
                 CPSF6 
                 BAGE3 
                 12 
                 21 
                 MCF7 
               
               
                 CPSF6 
                 BAGE3 
                 12 
                 21 
                 MCF7 
               
               
                 CPSF6 
                 C14orf135 
                 12 
                 14 
                 MCF7 
               
               
                 CPSF6 
                 CCT2 
                 12 
                 12 
                 MCF7 
               
               
                 CPSF6 
                 CNOT2 
                 12 
                 12 
                 MCF7 
               
               
                 CPSF6 
                 CSNK1D 
                 12 
                 17 
                 MCF7 
               
               
                 CPSF6 
                 HNRPDL 
                 12 
                 4 
                 MCF7 
               
               
                 CPSF6 
                 IVNS1ABP 
                 12 
                 1 
                 MCF7 
               
               
                 CPSF6 
                 LYZ 
                 12 
                 12 
                 MCF7 
               
               
                 CPSF6 
                 LYZ 
                 12 
                 12 
                 MCF7 
               
               
                 CPSF6 
                 LYZ 
                 12 
                 12 
                 MCF7 
               
               
                 CPSF6 
                 MDM2 
                 12 
                 12 
                 MCF7 
               
               
                 CPSF6 
                 NUP107 
                 12 
                 12 
                 MCF7 
               
               
                 CPSF6 
                 PGBD2 
                 12 
                 1 
                 MCF7 
               
               
                 CPSF6 
                 RPL3 
                 12 
                 22 
                 MCF7 
               
               
                 CPSF6 
                 RPL30 
                 12 
                 8 
                 MCF7 
               
               
                 CPSF6 
                 RPL30 
                 12 
                 8 
                 MCF7 
               
               
                 CPSF6 
                 SPG7 
                 12 
                 16 
                 MCF7 
               
               
                 NCOA3 
                 BCAS3 
                 20 
                 17 
                 MCF7 
               
               
                 NCOA3 
                 BCAS3 
                 20 
                 17 
                 MCF7 
               
               
                 NCOA3 
                 GNAS 
                 20 
                 20 
                 MCF7 
               
               
                 NCOA3 
                 H3F3A 
                 20 
                 1 
                 MCF7 
               
               
                 NCOA3 
                 H3F3A 
                 20 
                 1 
                 MCF7 
               
               
                 NCOA3 
                 NPL 
                 20 
                 1 
                 MCF7 
               
               
                 NCOA3 
                 TRIM33 
                 20 
                 1 
                 MCF7 
               
               
                 NOC4L 
                 CNIH4 
                 12 
                 1 
                 MCF7 
               
               
                 NOC4L 
                 EEF1D 
                 12 
                 8 
                 MCF7 
               
               
                 NOC4L 
                 FBRSL1 
                 12 
                 12 
                 MCF7 
               
               
                 NOC4L 
                 FBRSL1 
                 12 
                 12 
                 MCF7 
               
               
                 NOC4L 
                 FBRSL1 
                 12 
                 12 
                 MCF7 
               
               
                 NOC4L 
                 PTDSS2 
                 12 
                 11 
                 MCF7 
               
               
                 NOC4L 
                 PTDSS2 
                 12 
                 11 
                 MCF7 
               
               
                 NOC4L 
                 PXMP2 
                 12 
                 12 
                 MCF7 
               
               
                 NOC4L 
                 TMEM8A 
                 12 
                 16 
                 MCF7 
               
               
                 NOC4L 
                 ULK1 
                 12 
                 12 
                 MCF7 
               
               
                 SNHG3 
                 C2orf24 
                 1 
                 2 
                 MCF7 
               
               
                 SNHG3 
                 CCT3 
                 1 
                 1 
                 MCF7 
               
               
                 SNHG3 
                 CHAF1A 
                 1 
                 19 
                 MCF7 
               
               
                 SNHG3 
                 CRAMP1L 
                 1 
                 16 
                 MCF7 
               
               
                 SNHG3 
                 CRAMP1L 
                 1 
                 16 
                 MCF7 
               
               
                 SNHG3 
                 DNAJC11 
                 1 
                 1 
                 MCF7 
               
               
                 SNHG3 
                 GGPS1 
                 1 
                 1 
                 MCF7 
               
               
                 SNHG3 
                 GNAS 
                 1 
                 20 
                 MCF7 
               
               
                 SNHG3 
                 GTPBP4 
                 1 
                 10 
                 MCF7 
               
               
                 SNHG3 
                 LOC641298 
                 1 
                 16 
                 MCF7 
               
               
                 SNHG3 
                 MFF 
                 1 
                 2 
                 MCF7 
               
               
                 SNHG3 
                 MYBL2 
                 1 
                 20 
                 MCF7 
               
               
                 SNHG3 
                 NDUFS1 
                 1 
                 2 
                 MCF7 
               
               
                 SNHG3 
                 PDS5A 
                 1 
                 4 
                 MCF7 
               
               
                 SNHG3 
                 PDS5A 
                 1 
                 4 
                 MCF7 
               
               
                 SNHG3 
                 PRPF3 
                 1 
                 1 
                 MCF7 
               
               
                 SNHG3 
                 PRPF6 
                 1 
                 20 
                 MCF7 
               
               
                 SNHG3 
                 PSMB2 
                 1 
                 1 
                 MCF7 
               
               
                 SNHG3 
                 QRICH2 
                 1 
                 17 
                 MCF7 
               
               
                 SNHG3 
                 RNASEH1 
                 1 
                 2 
                 MCF7 
               
               
                 SNHG3 
                 SERINC2 
                 1 
                 1 
                 MCF7 
               
               
                 SNHG3 
                 SLC38A10 
                 1 
                 17 
                 MCF7 
               
               
                 SNHG3 
                 SYAP1 
                 1 
                 23 
                 MCF7 
               
               
                 SNHG3 
                 SYAP1 
                 1 
                 23 
                 MCF7 
               
               
                 SNHG3 
                 TCF25 
                 1 
                 16 
                 MCF7 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 MCF7 
               
               
                 SNHG3 
                 U2AF1 
                 1 
                 21 
                 MCF7 
               
               
                 SNHG3 
                 UIMC1 
                 1 
                 5 
                 MCF7 
               
               
                 SNHG3 
                 YIPF1 
                 1 
                 1 
                 MCF7 
               
               
                 TANC2 
                 CA4 
                 17 
                 17 
                 MCF7 
               
               
                 TANC2 
                 CA4 
                 17 
                 17 
                 MCF7 
               
               
                 TANC2 
                 CA4 
                 17 
                 17 
                 MCF7 
               
               
                 TANC2 
                 CA4 
                 17 
                 17 
                 MCF7 
               
               
                 TANC2 
                 CA4 
                 17 
                 17 
                 MCF7 
               
               
                 TANC2 
                 CA4 
                 17 
                 17 
                 MCF7 
               
               
                 TANC2 
                 FAF1 
                 17 
                 1 
                 MCF7 
               
               
                 TANC2 
                 GNAI3 
                 17 
                 1 
                 MCF7 
               
               
                 TANC2 
                 MRC2 
                 17 
                 17 
                 MCF7 
               
               
                 TANC2 
                 MRC2 
                 17 
                 17 
                 MCF7 
               
               
                 TANC2 
                 MRC2 
                 17 
                 17 
                 MCF7 
               
               
                 TANC2 
                 PVT1 
                 17 
                 8 
                 MCF7 
               
               
                 SNHG3 
                 AKR1A1 
                 1 
                 1 
                 SJCRH30 
               
               
                 SNHG3 
                 CCDC18 
                 1 
                 1 
                 SJCRH30 
               
               
                 SNHG3 
                 GNB2L1 
                 1 
                 5 
                 SJCRH30 
               
               
                 SNHG3 
                 KIF1B 
                 1 
                 1 
                 SJCRH30 
               
               
                 SNHG3 
                 MORF4L2 
                 1 
                 23 
                 SJCRH30 
               
               
                 SNHG3 
                 MTOR 
                 1 
                 1 
                 SJCRH30 
               
               
                 SNHG3 
                 NDUFAF4 
                 1 
                 6 
                 SJCRH30 
               
               
                 SNHG3 
                 OSBPL2 
                 1 
                 20 
                 SJCRH30 
               
               
                 SNHG3 
                 RPL5 
                 1 
                 1 
                 SJCRH30 
               
               
                 SNHG3 
                 SMARCC1 
                 1 
                 3 
                 SJCRH30 
               
               
                 SNHG3 
                 ZFR 
                 1 
                 5 
                 SJCRH30 
               
               
                 LOC375010 
                 DCUN1D4 
                 1 
                 4 
                 SK-N-SH 
               
               
                 LOC375010 
                 DCUN1D4 
                 1 
                 4 
                 SK-N-SH 
               
               
                 LOC375010 
                 GOLGA8B 
                 1 
                 15 
                 SK-N-SH 
               
               
                 LOC375010 
                 PIK3C3 
                 1 
                 18 
                 SK-N-SH 
               
               
                 LOC375010 
                 PVT1 
                 1 
                 8 
                 SK-N-SH 
               
               
                 LOC375010 
                 ZFR 
                 1 
                 5 
                 SK-N-SH 
               
               
                 PPP1R12C 
                 AKT2 
                 19 
                 19 
                 SK-N-SH 
               
               
                 PPP1R12C 
                 C19orf6 
                 19 
                 19 
                 SK-N-SH 
               
               
                 PPP1R12C 
                 CIRBP 
                 19 
                 19 
                 SK-N-SH 
               
               
                 PPP1R12C 
                 FKBP8 
                 19 
                 19 
                 SK-N-SH 
               
               
                 PPP1R12C 
                 GPC1 
                 19 
                 2 
                 SK-N-SH 
               
               
                 PPP1R12C 
                 HMGA2 
                 19 
                 12 
                 SK-N-SH 
               
               
                 PPP1R12C 
                 PNCK 
                 19 
                 23 
                 SK-N-SH 
               
               
                 PRKAR1B 
                 FAM20C 
                 7 
                 7 
                 SK-N-SH 
               
               
                 PRKAR1B 
                 MAFK 
                 7 
                 7 
                 SK-N-SH 
               
               
                 PRKAR1B 
                 PDGFA 
                 7 
                 7 
                 SK-N-SH 
               
               
                 PRKAR1B 
                 SUN1 
                 7 
                 7 
                 SK-N-SH 
               
               
                 PRKAR1B 
                 SUN1 
                 7 
                 7 
                 SK-N-SH 
               
               
                 SNHG3 
                 ATP6V1G2 
                 1 
                 6 
                 SK-N-SH 
               
               
                 SNHG3 
                 C11orf73 
                 1 
                 11 
                 SK-N-SH 
               
               
                 SNHG3 
                 CWF19L1 
                 1 
                 10 
                 SK-N-SH 
               
               
                 SNHG3 
                 DCI 
                 1 
                 16 
                 SK-N-SH 
               
               
                 SNHG3 
                 FSD1 
                 1 
                 19 
                 SK-N-SH 
               
               
                 SNHG3 
                 HNRNPC 
                 1 
                 14 
                 SK-N-SH 
               
               
                 SNHG3 
                 NMNAT1 
                 1 
                 1 
                 SK-N-SH 
               
               
                 SNHG3 
                 PDS5A 
                 1 
                 4 
                 SK-N-SH 
               
               
                 SNHG3 
                 RPLP0 
                 1 
                 12 
                 SK-N-SH 
               
               
                 SNHG3 
                 SENP3 
                 1 
                 17 
                 SK-N-SH 
               
               
                 SNHG3 
                 STIP1 
                 1 
                 11 
                 SK-N-SH 
               
               
                 SNHG3 
                 TRNAU1AP 
                 1 
                 1 
                 SK-N-SH 
               
               
                   
               
             
          
         
       
     
         [0137]    We have discovered a total of 98 such natural networks in 14 different cell lines ( FIG. 21 e   ). Table 9 has shown that there are 40 5′ natural networks in 10 cancer cell lines. And Table 8 has shown 58 3′ natural networks in 11 cancer cell lines. From Tables 8 and 9, we have observed that seven cell lines have both 5′ and 3′ networks. K562 cells have the most networks among the cancer cell lines, which have 30 such networks (10 5′ natural networks and 20 3′ natural networks) and count for 30% of the total identified natural networks. There is no doubt that K562 large RNA-seq datasets have contributed such abundant networks. However, the dataset sizes are not the dominate factor of identification of natural networks since both MCF-7 and SK-N-SH have much larger sequence datasets than K562 one ( FIG. 4 a   ). They have only 9 and 7 such natural networks, respectively. This suggests that such natural networks are characteristics of cancer types. 
         [0138]    As shown in Tables 8 and 9, we have compared 5′ and 3′ natural networks. Tables 8 and 9 have shown that there are significant differences between the 5′ and 3′ natural networks. These differences suggest that these natural networks of fusion transcripts may play very roles in cellular functions. 
         [0139]    Table 8 has shown that the 3′ most abundant network is involved with GNAS, which has highly complex imprinted expression pattern for guanine nucleotide regulatory protein and has been found to be associated with progressive osseous heteroplasia, and gnas hyperfunction. The GNAS natural networks have been found in 9 out of 11 cell lines. 
         [0140]    Table 9 has shown that the most abundant 5′ network is the one generated by SNHG3 and has been found in 9 out of 10 cancer cell lines. It is not surprising that Table 9 has shown that many genes for non-coding RNAs such as MIR17HG, DANCR (KIAA0114) and MCM3APAS have formed networks with other genes. The natural networks formed by non-coding RNAs have raised very possibilities that observed functions of many non-coding RNAs, such as mirRNAs (Ameres and Zamore 2013), are not functions of a single MIR gene, but the network formed by a non-coding RNA gene in certain cell types under certain different environments. 
         [0141]    As seen from above discussions, we have proposed that none-coding RNAs have organized networks to regulate large numbers of genes and to have more powerful roles in regulating multiple cellular functions in cell lines. We have selected the some non-coding RNA fusion transcripts for validations, one of which has been validated as shown in Table 4.  FIG. 22  has shown a schematic presentation of procedures to verify ncRNA00188|GNAI3 fusion transcripts. ncRNA00188 is non-coding RNA gene and is affiliated with the antisense RNA class. It has been known that GNAI3 gene coding for guanine nucleotide binding protein alpha inhibiting activity polypeptide 3, is associated with autosomal dominant Auriculocondylar syndrome (ARCND) and plays significant role in regulating downstream targets of the G protein-coupled endothelin receptor pathway (Oldham, et al. 2006). As shown in  FIG. 22 , ncRNA00188|GNAI3 fusion transcripts have first been detected in lymphoblastoid cells GM12878.  FIG. 22 a    shows that ncRNA00188 gene on the chromosome 17 and GNAI3 gene on the chromosome 1 have been brought together via translocation. Solid angle lines and dashed dots represent introns and gaps, respectively. Since read-though allows the generating fusion transcripts, it is not necessary that fusion genes may not have to be truncated and may be just close to each other. The total RNAs have been isolated from lymphoblastoid cells GM12878.  FIG. 22 b    has shown that junction sequences of ncRNA00188 and GNAI3 fusion junctions. Pre-mRNA splicing removes putative intron sequences to generate ncRNA00188|GNAI3 fusion transcripts. The primers based on fusion transcripts have been designed to amply ncRNA00188|GNAI3 cDNAs.  FIG. 22 c    shows that the ncRNA00188|GNAI3 fusion transcript is amplified by RT-PCR. cDNA fragments are then cloned into pCR4-TOPO clone vector. The positive clones are sequenced. The fusion transcripts are verified by blast and visual inspections.  FIG. 22 c    has shown the splice junctions of ncRNA00188|GNAI3 fusion transcripts. Arrow indicates splice junction sequences of the ncRNA00188|GNAI3 fusion transcripts. This has confirmed that the lymphoblastoid cells express non-coding RNA ncRNA00188|GNAI3 fusion transcripts. More systematic researches are required in the future to understand how these non-coding RNA fusion transcripts are regulated and expressed and to elucidate how these non-coding RNA fusion transcripts constitute natural networks to control and regulate the cell functions and how these natural networks transform the normal cells into cancer cells. 
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