# Patent

## Title
Nucleic acid compositions related to MIR-138-1-3P and uses thereof

## Abstract

Described herein are polynucleotides associated with prostate and lung cancer. The polynucleotides are miRNAs and miRNA precursors. Related methods and compositions that can be used for diagnosis, prognosis, and treatment of those medical conditions are disclosed. Also described herein are methods that can be used to identify modulators of prostate and lung cancer.

## Background
FIELD OF THE INVENTION
The invention relates in general to microRNA molecules as well as various nucleic acid molecules relating thereto or derived therefrom.
REFERENCES TO THE SEQUENCE LISTING AND TABLES
Applicant hereby makes reference to the sequence listing and tables that were submitted electronically via EFS-Web. The sequence listing consists of a filed named “Sequence-Listing.txt,” (14 KB), created on May 3, 2017. The tables consist of the following files: “Table1.txt” (1 KB), which was created on May 3, 2017; and “Table2.txt” (2 KB), “Table3.txt” (1 KB), “Table4.txt” (6 KB), “Table1.txt” (1 KB), “Table6.txt” (38 KB), “Table1.txt” (2 KB), “Table1.txt” (4 KB), “Table9.txt” (190 KB), which were created on May 2, 2017. The sequence listing and tables are all incorporated herein by reference. 







TABLES




The patent contains table(s) that have been included at the end of the specification.






BACKGROUND OF THE INVENTION
MicroRNAs (miRNAs) are short RNA oligonucleotides of approximately 22 nucleotides that are involved in gene regulation. MicroRNAs regulate gene expression by targeting mRNAs for cleavage or translational repression. Although miRNAs are present in a wide range of species including C. elegans, Drosophila and humans, they have only recently been identified. More importantly, the role of miRNAs in the development and progression of disease has only recently become appreciated.
As a result of their small size, miRNAs have been difficult to identify using standard methodologies. A limited number of miRNAs have been identified by extracting large quantities of RNA. MiRNAs have also been identified that contribute to the presentation of visibly discernable phenotypes. Expression array data shows that miRNAs are expressed in different developmental stages or in different tissues. The restriction of miRNAs to certain tissues or at limited developmental stages indicates that the miRNAs identified to date are likely only a small fraction of the total miRNAs.
Computational approaches have recently been developed to identify the remainder of miRNAs in the genome. Tools such as MiRscan and MiRseeker have identified miRNAs that were later experimentally confirmed. Based on these computational tools, it has been estimated that the human genome contains 200-255 miRNA genes. These estimates are based on an assumption, however, that the miRNAs remaining to be identified will have the same properties as those miRNAs already identified. Based on the fundamental importance of miRNAs in mammalian biology and disease, the art needs to identify unknown miRNAs. The present invention satisfies this need and provides a significant number of miRNAs and uses therefore.
SUMMARY OF THE INVENTION
The present invention is related to an isolated nucleic acid comprising a sequence of a pri-miRNA, pre-miRNA, miRNA, miRNA*, anti-miRNA, or a miRNA binding site, or a variant thereof. The nucleic acid may comprise the sequence of a hairpin referred to in Table 1; the sequence of a miRNA referred to in Table 1; the sequence of a target gene binding site referred to in Table 4; or a sequence comprising at least 12 contiguous nucleotides at least 60% identical thereto. The isolated nucleic acid may be from 5-250 nucleotides in length.
The present invention is also related to a probe comprising the nucleic acid. The probe may comprise at least 8-22 contiguous nucleotides complementary to a miRNA referred to in Table 2 as differentially expressed in prostate cancer or lung cancer.
The present invention is also related to a plurality of the probes. The plurality of probes may comprise at least one probe complementary to each miRNA referred to in Table 2 as differentially expressed in prostate cancer. The plurality of probes may also comprise at least one probe complementary to each miRNA referred to in Table 2 as differentially expressed in lung cancer.
The present invention is also related to a composition comprising a probe or plurality of probes.
The present invention is also related to a biochip comprising a solid substrate, said substrate comprising a plurality of probes. Each of the probes may be attached to the substrate at a spatially defined address. The biochip may comprise probes that are complementary to a miRNA referred to in Table 2 as differentially expressed in prostate cancer. The biochip may also comprise probes that are complementary to a miRNA referred to in Table 2 as differentially expressed in lung cancer.
The present invention is also related to a method of detecting differential expression of a disease-associated miRNA. A biological sample may be provide and the level of a nucleic acid measured that is at least 70% identical to a sequence of a miRNA referred to in Table 1; or variants thereof. A difference in the level of the nucleic acid compared to a control is indicative of differential expression.
The present invention is also related to a method of identifying a compound that modulates a pathological condition. A cell may be provided that is capable of expressing a nucleic acid at least 70% identical to a sequence of a miRNA referred to in Table 1 or variants thereof. The cell may be contacted with a candidate modulator and then measuring the level of expression of the nucleic acid. A difference in the level of the nucleic acid compared to a control identifies the compound as a modulator of a pathological condition associated with the nucleic acid.
The present invention is also related to a method of inhibiting expression of a target gene in a cell. Into the cell, a nucleic acid may be introduced in an amount sufficient to inhibit expression of the target gene. The target gene may comprise a binding site substantially identical to a binding site referred to in Table 4; or a variant thereof. The nucleic acid may comprise a sequence of one of SEQ ID NOS: 1-4; or a variant thereof. Expression of the target gene may be inhibited in vitro or in vivo.
The present invention is also related to a method of increasing expression of a target gene in a cell. Into the cell, a nucleic acid may be introduced in an amount sufficient to inhibit expression of the target gene. The target gene may comprise a binding site substantially identical to a binding site referred to in Table 4; or a variant thereof. The nucleic acid may comprise a sequence substantially complementary to one of SEQ ID NOS: 1-4; or a variant thereof. Expression of the target gene may be inhibited in vitro or in vivo. Expression of the target gene may be increased in vitro or in vivo.
The present invention is also related to a method of treating a patient with a disorder set forth on Table 6 comprising administering to a patient in need thereof a nucleic acid comprising a sequence of one of SEQ ID NOS: 1-4; or a variant thereof.



BRIEF DESCRIPTION OF THE DRAWINGS
FIGS. 1A-1C demonstrate a model of maturation for miRNAs.
FIG. 2A shows a schematic illustration of the MC19cluster on 19q13.42. FIG. 2A shows the  ̃500,000 bp region of chromosome 19, from 58,580,001 to 59,080,000 (according to the May 2004 USCS assembly), in which the cluster is located including the neighboring protein-coding genes. The MC19-1 cluster is indicated by a rectangle. Mir-371, mir-372, and mir-373 are indicted by lines. Protein coding genes flanking the cluster are represented by large arrow-heads. FIG. 2B shows a detailed structure of the MC19-1 miRNA cluster. A region of  ̃102,000 bp, from 58,860,001 to 58,962,000 (according to the May 2004 USCS assembly), is presented. MiRNA precursors are represented by a black bars. It should be noted that all miRNAs are at the same orientation from left to right. Shaded areas around miRNA precursors represent repeating units in which the precursor is embedded. The location of mir-371, mir-372, and mir-373, is also presented.
FIGS. 3A-3B are a graphical representation of multiple sequence alignment of 35 human repeat units at distinct size of  ̃690 nt (FIG. 3A) and 26 chimpanzees repeat units (FIG. 3B). The graph was generated by calculating a similarity score for each position in the alignment with an averaging sliding window of 10 nt (Maximum score −1, minimum score-0). The repeat unit sequences were aligned by ClustalW program. Each position of the resulting alignment was assigned a score which represented the degree of similarity at this position. The region containing the miRNA precursors is bordered by vertical lines. The exact location of the mature miRNAs derived from the 5′ stems (5p) and 3′ stems (3p) of the precursors is indicted by vertical lines.
FIGS. 4A-4C show sequence alignments of the 43 A-type pre-miRNAs of the MC19-1 cluster. FIG. 4A shows the multiple sequence alignment with the Position of the mature miRNAs marked by a frame. The consensus sequence is shown at the bottom. Conserved nucleotides are colored as follows: black-100%, dark grey—80% to 99%, and clear grey—60% to 79%. FIG. 4B shows alignments of consensus mature A-type miRNAs with the upstream human cluster of mir-371, mir-372, miR-373. FIG. 4C shows alignments of consensus mature A-type miRNAs with the hsa-mir-371-373 mouse orthologous cluster. The miRNAs hsa-miR-A1 through hsa-miR-A43 of FIG. 4A have SEQ ID NOs: 13 through 66, respectively. In FIG. 4B, the following miRNAs have the following sequences: hsa-miR-371, 3p (SEQ ID NO: 67), hsa-miR-372, 3p (SEQ ID NO: 68), hsa-miR-373, 3p (SEQ ID NO: 69), hsa-miR-A-3p (consensus)(SEQ ID NO: 70), hsa-miR-373-5-p (SEQ ID NO: 71), hsa-miR-A-5p (consensus)(SEQ ID NO: 77). In FIG. 4C, the following miRNAs have the following sequences: hsa-miR-302a (SEQ ID NO: 72), hsa-miR-302b (SEQ ID NO: 73), hsa-miR-302c (SEQ ID NO: 74), hsa-miR-302d (SEQ ID NO: 75), and hsa-miR-A-3p (consensus)(SEQ ID NO: 76). FIGS. 5A-C show expression analysis of the MC19-1 miRNAs. FIG. 5A shows a Northern blot analysis of two selected A-type miRNAs. Expression was analyzed using total RNA from human brain (B), liver (L), thymus (T), placenta (P) and HeLa cells (H). The expression of mir-98 and ethidium bromide staining of the tRNA band served as control. FIG. 5B shows RT-PCR analysis of the mRNA transcript containing the A-type miRNA precursors. Reverse transcription of 5 μg total RNA from placenta was performed using oligo-dT. This was followed by PCR using the denoted primers (indicated by horizontal arrows). The region examined is illustrated at the top. Vertical black bars represent the pre-miRNA; shaded areas around the pre-miRNAs represent the repeating units; the location of four ESTs is indicted at the right side; the poly-A site, as found in the ESTs and located downstream to an AATAAA consensus, is indicated by a vertical arrow. The fragments expected from RT-PCR using three primer combinations are indicated below the illustration of the cluster region. The results of the RT-PCR analysis are presented below the expected fragments. FIG. 5C shows the sequencing strategy of the FR2 fragment. The fragment was cloned into the pTZ57R\T vector and sequenced using external and internal primers.



DETAILED DESCRIPTION
The present invention provides nucleotide sequences of miRNAs, precursors thereto, targets thereof and related sequences. Such nucleic acids are useful for diagnostic purposes, and also for modifying target gene expression. Other aspects of the invention will become apparent to the skilled artisan by the following description of the invention.
1. Definitions
Before the present compounds, products and compositions and methods are disclosed and described, it is to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting. It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.
a. Animal
“Animal” as used herein may mean fish, amphibians, reptiles, birds, and mammals, such as mice, rats, rabbits, goats, cats, dogs, cows, apes and humans.
b. Attached
“Attached” or “immobilized” as used herein to refer to a probe and a solid support may mean that the binding between the probe and the solid support is sufficient to be stable under conditions of binding, washing, analysis, and removal. The binding may be covalent or non-covalent. Covalent bonds may be formed directly between the probe and the solid support or may be formed by a cross linker or by inclusion of a specific reactive group on either the solid support or the probe or both molecules. Non-covalent binding may be one or more of electrostatic, hydrophilic, and hydrophobic interactions. Included in non-covalent binding is the covalent attachment of a molecule, such as streptavidin, to the support and the non-covalent binding of a biotinylated probe to the streptavidin. Immobilization may also involve a combination of covalent and non-covalent interactions.
c. Biological Sample
“Biological sample” as used herein may mean a sample of biological tissue or fluid that comprises nucleic acids. Such samples include, but are not limited to, tissue isolated from animals. Biological samples may also include sections of tissues such as biopsy and autopsy samples, frozen sections taken for histologic purposes, blood, plasma, serum, sputum, stool, tears, mucus, hair, and skin. Biological samples also include explants and primary and/or transformed cell cultures derived from patient tissues. A biological sample may be provided by removing a sample of cells from an animal, but can also be accomplished by using previously isolated cells (e.g., isolated by another person, at another time, and/or for another purpose), or by performing the methods of the invention in vivo. Archival tissues, such as those having treatment or outcome history, may also be used.
d. Complement
“Complement” or “complementary” as used herein may mean Watson-Crick or Hoogsteen base pairing between nucleotides or nucleotide analogs of nucleic acid molecules.
e. Differential Expression
“Differential expression” may mean qualitative or quantitative differences in the temporal and/or cellular gene expression patterns within and among cells and tissue. Thus, a differentially expressed gene can qualitatively have its expression altered, including an activation or inactivation, in, e.g., normal versus disease tissue. Genes may be turned on or turned off in a particular state, relative to another state thus permitting comparison of two or more states. A qualitatively regulated gene will exhibit an expression pattern within a state or cell type which may be detectable by standard techniques. Some genes will be expressed in one state or cell type, but not in both. Alternatively, the difference in expression may be quantitative, e.g., in that expression is modulated, either up-regulated, resulting in an increased amount of transcript, or down-regulated, resulting in a decreased amount of transcript. The degree to which expression differs need only be large enough to quantify via standard characterization techniques such as expression arrays, quantitative reverse transcriptase PCR, northern analysis, and RNase protection.
f. Gene
“Gene” used herein may be a genomic gene comprising transcriptional and/or translational regulatory sequences and/or a coding region and/or non-translated sequences (e.g., introns, 5′- and 3′-untranslated sequences). The coding region of a gene may be a nucleotide sequence coding for an amino acid sequence or a functional RNA, such as tRNA, rRNA, catalytic RNA, siRNA, miRNA and antisense RNA. A gene may also be an mRNA or cDNA corresponding to the coding regions (e.g., exons and miRNA) optionally comprising 5′- or 3′-untranslated sequences linked thereto. A gene may also be an amplified nucleic acid molecule produced in vitro comprising all or a part of the coding region and/or 5′- or 3′-untranslated sequences linked thereto.
g. Host Cell
“Host cell” used herein may be a naturally occurring cell or a transformed cell that contains a vector and supports the replication of the vector. Host cells may be cultured cells, explants, cells in vivo, and the like. Host cells may be prokaryotic cells such as E. coli, or eukaryotic cells such as yeast, insect, amphibian, or mammalian cells, such as CHO, HeLa.
h. Identity
“Identical” or “identity” as used herein in the context of two or more nucleic acids or polypeptide sequences, may mean that the sequences have a specified percentage of nucleotides or amino acids that are the same over a specified region. The percentage may be calculated by comparing optimally aligning the two sequences, comparing the two sequences over the specified region, determining the number of positions at which the identical residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the specified region, and multiplying the result by 100 to yield the percentage of sequence identity. In cases where the two sequences are of different lengths or the alignment produces staggered end and the specified region of comparison includes only a single sequence, the residues of single sequence are included in the denominator but not the numerator of the calculation. When comparing DNA and RNA, thymine (T) and uracil (U) are considered equivalent. Identity may be performed manually or by using computer sequence algorithm such as BLAST or BLAST 2.0.
i. Label
“Label” as used herein may mean a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means. For example, useful labels include 32P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and other entities which can be made detectable. A label may be incorporated into nucleic acids and proteins at any position.
j. Nucleic Acid
“Nucleic acid” or “oligonucleotide” or “polynucleotide” used herein may mean at least two nucleotides covalently linked together. As will be appreciated by those in the art, the depiction of a single strand also defines the sequence of the complementary strand. Thus, a nucleic acid also encompasses the complementary strand of a depicted single strand. As will also be appreciated by those in the art, many variants of a nucleic acid may be used for the same purpose as a given nucleic acid. Thus, a nucleic acid also encompasses substantially identical nucleic acids and complements thereof. As will also be appreciated by those in the art, a single strand provides a probe for a probe that may hybridize to the target sequence under stringent hybridization conditions. Thus, a nucleic acid also encompasses a probe that hybridizes under stringent hybridization conditions.
Nucleic acids may be single stranded or double stranded, or may contain portions of both double stranded and single stranded sequence. The nucleic acid may be DNA, both genomic and cDNA, RNA, or a hybrid, where the nucleic acid may contain combinations of deoxyribo- and ribo-nucleotides, and combinations of bases including uracil, adenine, thymine, cytosine, guanine, inosine, xanthine hypoxanthine, isocytosine and isoguanine. Nucleic acids may be obtained by chemical synthesis methods or by recombinant methods.
A nucleic acid will generally contain phosphodiester bonds, although nucleic acid analogs may be included that may have at least one different linkage, e.g., phosphoramidate, phosphorothioate, phosphorodithioate, or O-methylphosphoroamidite linkages and peptide nucleic acid backbones and linkages. Other analog nucleic acids include those with positive backbones; non-ionic backbones, and non-ribose backbones, including those described in U.S. Pat. Nos. 5,235,033 and 5,034,506, which are incorporated by reference. Nucleic acids containing one or more non-naturally occurring or modified nucleotides are also included within one definition of nucleic acids. The modified nucleotide analog may be located for example at the 5′-end and/or the 3′-end of the nucleic acid molecule. Representative examples of nucleotide analogs may be selected from sugar- or backbone-modified ribonucleotides. It should be noted, however, that also nucleobase-modified ribonucleotides, i.e. ribonucleotides, containing a non-naturally occurring nucleobase instead of a naturally occurring nucleobase such as uridines or cytidines modified at the 5-position, e.g. 5-(2-amino)propyl uridine, 5-bromo uridine; adenosines and guanosines modified at the 8-position, e.g. 8-bromo guanosine; deaza nucleotides, e.g. 7-deaza-adenosine; O- and N-alkylated nucleotides, e.g. N6-methyl adenosine are suitable. The 2′-OH-group may be replaced by a group selected from H, OR, R, halo, SH, SR, NH2, NHR, NR2 or CN, wherein R is C1-C6 alkyl, alkenyl or alkynyl and halo is F, Cl, Br or I. Modifications of the ribose-phosphate backbone may be done for a variety of reasons, e.g., to increase the stability and half-life of such molecules in physiological environments or as probes on a biochip. Mixtures of naturally occurring nucleic acids and analogs may be made; alternatively, mixtures of different nucleic acid analogs, and mixtures of naturally occurring nucleic acids and analogs may be made.
k. Operably Linked
“Operably linked” used herein may mean that expression of a gene is under the control of a promoter with which it is spatially connected. A promoter may be positioned 5′ (upstream) or 3′ (downstream) of the gene under its control. The distance between the promoter and the gene may be approximately the same as the distance between that promoter and the gene it controls in the gene from which the promoter is derived. As is known in the art, variation in this distance can be accommodated without loss of promoter function.
l. Probe
“Probe” as used herein may mean an oligonucleotide capable of binding to a target nucleic acid of complementary sequence through one or more types of chemical bonds, usually through complementary base pairing, usually through hydrogen bond formation. Probes may bind target sequences lacking complete complementarity with the probe sequence depending upon the stringency of the hybridization conditions. There may be any number of base pair mismatches which will interfere with hybridization between the target sequence and the single stranded nucleic acids of the present invention. However, if the number of mutations is so great that no hybridization can occur under even the least stringent of hybridization conditions, the sequence is not a complementary target sequence. A probe may be single stranded or partially single and partially double stranded. The strandedness of the probe is dictated by the structure, composition, and properties of the target sequence. Probes may be directly labeled or indirectly labeled such as with biotin to which a streptavidin complex may later bind.
m. Promoter
“Promoter” as used herein may mean a synthetic or naturally-derived molecule which is capable of conferring, activating or enhancing expression of a nucleic acid in a cell. A promoter may comprise one or more specific regulatory elements to further enhance expression and/or to alter the spatial expression and/or temporal expression of same. A promoter may also comprise distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription. A promoter may be derived from sources including viral, bacterial, fungal, plants, insects, and animals. A promoter may regulate the expression of a gene component constitutively, or differentially with respect to cell, the tissue or organ in which expression occurs or, with respect to the developmental stage at which expression occurs, or in response to external stimuli such as physiological stresses, pathogens, metal ions, or inducing agents. Representative examples of promoters include the bacteriophage T7 promoter, bacteriophage T3 promoter, SP6 promoter, lac operator-promoter, tac promoter, SV40 late promoter, SV40 early promoter, RSV-LTR promoter, CMV IE promoter, SV40 early promoter or SV40 late promoter and the CMV IE promoter.
n. Selectable Marker
“Selectable marker” used herein may mean any gene which confers a phenotype on a cell in which it is expressed to facilitate the identification and/or selection of cells which are transfected or transformed with a genetic construct. Representative examples of selectable markers include the ampicillin-resistance gene (Ampr), tetracycline-resistance gene (Tcr), bacterial kanamycin-resistance gene (Kanr), zeocin resistance gene, the AURI-C gene which confers resistance to the antibiotic aureobasidin A, phosphinothricin-resistance gene, neomycin phosphotransferase gene (nptII), hygromycin-resistance gene, beta-glucuronidase (GUS) gene, chloramphenicol acetyltransferase (CAT) gene, green fluorescent protein-encoding gene and luciferase gene.
o. Stringent Hybridization Conditions
“Stringent hybridization conditions” used herein may mean conditions under which a first nucleic acid sequence (e.g., probe) will hybridize to a second nucleic acid sequence (e.g., target), such as in a complex mixture of nucleic acids, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH. The Tm may be the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). Stringent conditions may be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01-1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., about 10-50 nucleotides) and at least about 60° C. for long probes (e.g., greater than about 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal may be at least 2 to 10 times background hybridization. Exemplary stringent hybridization conditions include the following: 50% formamide, 5×SSC, and 1% SDS, incubating at 42° C., or, 5×SSC, 1% SDS, incubating at 65° C., with wash in 0.2×SSC, and 0.1% SDS at 65° C.
p. Substantially Complementary
“Substantially complementary” used herein may mean that a first sequence is at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical to the complement of a second sequence over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more nucleotides, or that the two sequences hybridize under stringent hybridization conditions.
q. Substantially Identical
“Substantially identical” used herein may mean that a first and second sequence are at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98% or 99% identical over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more nucleotides or amino acids, or with respect to nucleic acids, if the first sequence is substantially complementary to the complement of the second sequence.
r. Target
“Target” as used herein may mean a polynucleotide that may be bound by one or more probes under stringent hybridization conditions.
s. Terminator
“Terminator” used herein may mean a sequence at the end of a transcriptional unit which signals termination of transcription. A terminator may be a 3′-non-translated DNA sequence containing a polyadenylation signal, which may facilitate the addition of polyadenylate sequences to the 3′-end of a primary transcript. A terminator may be derived from sources including viral, bacterial, fungal, plants, insects, and animals. Representative examples of terminators include the SV40 polyadenylation signal, HSV TK polyadenylation signal, CYC1 terminator, ADH terminator, SPA terminator, nopaline synthase (NOS) gene terminator of Agrobacterium tumefaciens, the terminator of the Cauliflower mosaic virus (CaMV) 35S gene, the zein gene terminator from Zea mays, the Rubisco small subunit gene (SSU) gene terminator sequences, subclover stunt virus (SCSV) gene sequence terminators, rho-independent E. coli terminators, and the lacZ alpha terminator.
t. Vector
“Vector” used herein may mean a nucleic acid sequence containing an origin of replication. A vector may be a plasmid, bacteriophage, bacterial artificial chromosome or yeast artificial chromosome. A vector may be a DNA or RNA vector. A vector may be either a self-replicating extrachromosomal vector or a vector which integrate into a host genome.
2. MicroRNA
While not being bound by theory, the current model for the maturation of mammalian miRNAs is shown in FIG. 1. A gene coding for a miRNA may be transcribed leading to production of an miRNA precursor known as the pri-miRNA. The pri-miRNA may be part of a polycistronic RNA comprising multiple pri-miRNAs. The pri-miRNA may form a hairpin with a stem and loop. As indicated on FIG. 1, the stem may comprise mismatched bases.
The hairpin structure of the pri-miRNA may be recognized by Drosha, which is an RNase III endonuclease. Drosha may recognize terminal loops in the pri-miRNA and cleave approximately two helical turns into the stem to produce a 60-70 nt precursor known as the pre-miRNA. Drosha may cleave the pri-miRNA with a staggered cut typical of RNase III endonucleases yielding a pre-miRNA stem loop with a 5′ phosphate and  ̃2 nucleotide 3′ overhang. Approximately one helical turn of stem ( ̃10 nucleotides) extending beyond the Drosha cleavage site may be essential for efficient processing. The pre-miRNA may then be actively transported from the nucleus to the cytoplasm by Ran-GTP and the export receptor Ex-portin-5.
The pre-miRNA may be recognized by Dicer, which is also an RNase III endonuclease. Dicer may recognize the double-stranded stem of the pre-miRNA. Dicer may also recognize the 5′ phosphate and 3′ overhang at the base of the stem loop. Dicer may cleave off the terminal loop two helical turns away from the base of the stem loop leaving an additional 5′ phosphate and  ̃2 nucleotide 3′ overhang. The resulting siRNA-like duplex, which may comprise mismatches, comprises the mature miRNA and a similar-sized fragment known as the miRNA*. The miRNA and miRNA* may be derived from opposing arms of the pri-miRNA and pre-miRNA. MiRNA* sequences may be found in libraries of cloned miRNAs but typically at lower frequency than the miRNAs.
Although initially present as a double-stranded species with miRNA*, the miRNA may eventually become incorporated as single-stranded RNAs into a ribonucleoprotein complex known as the RNA-induced silencing complex (RISC). Various proteins can form the RISC, which can lead to variability in specifity for miRNA/miRNA* duplexes, binding site of the target gene, activity of miRNA (repress or activate), which strand of the miRNA/miRNA* duplex is loaded in to the RISC.
When the miRNA strand of the miRNA:miRNA* duplex is loaded into the RISC, the miRNA* may be removed and degraded. The strand of the miRNA:miRNA* duplex that is loaded into the RISC may be the strand whose 5′ end is less tightly paired. In cases where both ends of the miRNA:miRNA* have roughly equivalent 5′ pairing, both miRNA and miRNA* may have gene silencing activity.
The RISC may identify target nucleic acids based on high levels of complementarity between the miRNA and the mRNA, especially by nucleotides 2-8 of the miRNA. Only one case has been reported in animals where the interaction between the miRNA and its target was along the entire length of the miRNA. This was shown for mir-196 and Hox B8 and it was further shown that mir-196 mediates the cleavage of the Hox B8 mRNA (Yekta et al 2004, Science 304-594). Otherwise, such interactions are known only in plants (Bartel & Bartel 2003, Plant Physiol 132-709).
A number of studies have looked at the base-pairing requirement between miRNA and its mRNA target for achieving efficient inhibition of translation (reviewed by Bartel 2004, Cell 116-281). In mammalian cells, the first 8 nucleotides of the miRNA may be important (Doench & Sharp 2004 GenesDev 2004-504). However, other parts of the microRNA may also participate in mRNA binding. Moreover, sufficient base pairing at the 3′ can compensate for insufficient pairing at the 5′ (Brennecke at al, 2005 PLoS 3-e85). Computation studies, analyzing miRNA binding on whole genomes have suggested a specific role for bases 2-7 at the 5′ of the miRNA in target binding but the role of the first nucleotide, found usually to be “A” was also recognized (Lewis et at 2005 Cell 120-15). Similarly, nucleotides 1-7 or 2-8 were used to identify and validate targets by Krek et al (2005, Nat Genet 37-495).
The target sites in the mRNA may be in the 5′ UTR, the 3′ UTR or in the coding region. Interestingly, multiple miRNAs may regulate the same mRNA target by recognizing the same or multiple sites. The presence of multiple miRNA complementarity sites in most genetically identified targets may indicate that the cooperative action of multiple RISCs provides the most efficient translational inhibition.
MiRNAs may direct the RISC to downregulate gene expression by either of two mechanisms: mRNA cleavage or translational repression. The miRNA may specify cleavage of the mRNA if the mRNA has a certain degree of complementarity to the miRNA. When a miRNA guides cleavage, the cut may be between the nucleotides pairing to residues 10 and 11 of the miRNA. Alternatively, the miRNA may repress translation if the miRNA does not have the requisite degree of complementarity to the miRNA. Translational repression may be more prevalent in animals since animals may have a lower degree of complementarity.
It should be notes that there may be variability in the 5′ and 3′ ends of any pair of miRNA and miRNA*. This variability may be due to variability in the enzymatic processing of Drosha and Dicer with respect to the site of cleavage. Variability at the 5′ and 3′ ends of miRNA and miRNA* may also be due to mismatches in the stem structures of the pri-miRNA and pre-miRNA. The mismatches of the stem strands may lead to a population of different hairpin structures. Variability in the stem structures may also lead to variability in the products of cleavage by Drosha and Dicer.
3. Nucleic Acid
The present invention relates to an isolated nucleic acid comprising a nucleotide sequence referred to in SEQ ID NOS: 1-4, or variants thereof. The variant may be a complement of the referenced nucleotide sequence. The variant may also be a nucleotide sequence that is substantially identical to the referenced nucleotide sequence or the complement thereof. The variant may also be a nucleotide sequence which hybridizes under stringent conditions to the referenced nucleotide sequence, complements thereof, or nucleotide sequences substantially identical thereto.
The nucleic acid may have a length of from 10 to 100 nucleotides. The nucleic acid may have a length of at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80 or 90 nucleotides. The nucleic acid may be synthesized or expressed in a cell (in vitro or in vivo) using a synthetic gene described below. The nucleic acid may be synthesized as a single strand molecule and hybridized to a substantially complementary nucleic acid to form a duplex, which is considered a nucleic acid of the invention. The nucleic acid may be introduced to a cell, tissue or organ in a single- or double-stranded form or capable of being expressed by a synthetic gene using methods well known to those skilled in the art, including as described in U.S. Pat. No. 6,506,559 which is incorporated by reference.
a. Pri-miRNA
The nucleic acid of the invention may comprise a sequence of a pri-miRNA or a variant thereof. The pri-miRNA sequence may comprise from 45-250, 55-200, 70-150 or 80-100 nucleotides. The sequence of the pri-miRNA may comprise a pre-miRNA, miRNA and miRNA* as set forth below. The pri-miRNA may also comprise a miRNA or miRNA* and the complement thereof, and variants thereof. The pri-miRNA may comprise at least 19% adenosine nucleotides, at least 16% cytosine nucleotides, at least 23% thymine nucleotides and at least 19% guanine nucleotides.
The pri-miRNA may form a hairpin structure. The hairpin may comprise a first and second nucleic acid sequence that are substantially complimentary. The first and second nucleic acid sequence may be from 37-50 nucleotides. The first and second nucleic acid sequence may be separated by a third sequence of from 8-12 nucleotides. The hairpin structure may have a free energy less than −25 Kcal/mole as calculated by the Vienna algorithm with default parameters, as described in Hofacker et al., Monatshefte f. Chemie 125: 167-188 (1994), the contents of which are incorporated herein. The hairpin may comprise a terminal loop of 4-20, 8-12 or 10 nucleotides.
The sequence of the pri-miRNA may comprise the sequence of a hairpin referred to in Table 1, or variants thereof. The numerical identifiers for HID (hairpins) and MID (miRNAs) in Tables 1-9 correspond to SEQ ID NOS: 1-4 as follows.







TABLE 10







MID Sequence Identifiers










HID Numerical Identifier
SEQ ID NO







778
1

















TABLE 11







HID Sequence Identifiers










MID Numerical Identifier
SEQ ID NO







8545
2



8546
3



8547
4










The MID and HID numerical identifiers in the tables above refer to the hairpins and miRNAs with the same numerical identifiers described in Tables 1-10 of U.S. Patent Publication No. 2016/0046935, the contents of which are incorporated herein by reference, and use the same numbers as the sequence identifiers in the sequence listing of U.S. Patent Publication No. 2016/0046935, the contents of which are incorporated herein by reference.
b. Pre-miRNA
The nucleic acid of the invention may also comprise a sequence of a pre-miRNA or a variant thereof. The pre-miRNA sequence may comprise from 45-90, 60-80 or 60-70 nucleotides. The sequence of the pre-miRNA may comprise a miRNA and a miRNA* as set forth below. The pre-miRNA may also comprise a miRNA or miRNA* and the complement thereof, and variants thereof. The sequence of the pre-miRNA may also be that of a pri-miRNA excluding from 0-160 nucleotides from the 5′ and 3′ ends of the pri-miRNA.
The sequence of the pre-miRNA may comprise the sequence of a hairpin referred to in Table 1, or variants thereof.
c. MiRNA
The nucleic acid of the invention may also comprise a sequence of a miRNA, miRNA* or a variant thereof. The miRNA sequence may comprise from 13-33, 18-24 or 21-23 nucleotides. The sequence of the miRNA may be the first 13-33 nucleotides of the pre-miRNA. The sequence of the miRNA may be the last 13-33 nucleotides of the pre-miRNA.
The sequence of the miRNA may comprise the sequence of a miRNA referred to in Table 1, or variants thereof.
d. Anti-miRNA
The nucleic acid of the invention may also comprise a sequence of an anti-miRNA that is capable of blocking the activity of a miRNA or miRNA*. The anti-miRNA may comprise a total of 5-100 or 10-60 nucleotides. The anti-miRNA may also comprise a total of at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or 26 nucleotides. The sequence of the anti-miRNA may comprise (a) at least 5 nucleotides that are substantially identical to the 5′ of a miRNA and at least 5-12 nucleotide that are substantially complimentary to the flanking regions of the target site from the 5′ end of said miRNA, or (b) at least 5-12 nucleotides that are substantially identical to the 3′ of a miRNA and at least 5 nucleotide that are substantially complimentary to the flanking region of the target site from the 3′ end of said miRNA.
The sequence of the anti-miRNA may comprise the compliment of a sequence of a miRNA referred to in Table 1, or variants thereof.
e. Binding Site of Target
The nucleic acid of the invention may also comprise a sequence of a target miRNA binding site, or a variant thereof. The target site sequence may comprise a total of 5-100 or 10-60 nucleotides. The target site sequence may comprise at least 5 nucleotides of the sequence of a target gene binding site referred to in Table 4, or variants thereof.
4. Synthetic Gene
The present invention also relates to a synthetic gene comprising a nucleic acid of the invention operably linked to a transcriptional and/or translational regulatory sequences. The synthetic gene may be capable of modifying the expression of a target gene with a binding site for the nucleic acid of the invention. Expression of the target gene may be modified in a cell, tissue or organ. The synthetic gene may be synthesized or derived from naturally-occurring genes by standard recombinant techniques. The synthetic gene may also comprise terminators at the 3′-end of the transcriptional unit of the synthetic gene sequence. The synthetic gene may also comprise a selectable marker.
5. Vector
The present invention also relates to a vector comprising a synthetic gene of the invention. The vector may be an expression vector. An expression vector may comprise additional elements. For example, the expression vector may have two replication systems allowing it to be maintained in two organisms, e.g., in mammalian or insect cells for expression and in a prokaryotic host for cloning and amplification. For integrating expression vectors, the expression vector may contain at least one sequence homologous to the host cell genome, and preferably two homologous sequences which flank the expression construct. The integrating vector may be directed to a specific locus in the host cell by selecting the appropriate homologous sequence for inclusion in the vector. The vector may also comprise a selectable marker gene to allow the selection of transformed host cells.
6. Host Cell
The present invention also relates to a host cell comprising a vector of the invention. The cell may be a bacterial, fungal, plant, insect or animal cell.
7. Probes
The present invention also relates to a probe comprising a nucleic acid of the invention. Probes may be used for screening and diagnostic methods, as outlined below. The probe may be attached or immobilized to a solid substrate, such as a biochip.
The probe may have a length of from 8 to 500, 10 to 100 or 20 to 60 nucleotides. The probe may also have a length of at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280 or 300 nucleotides. The probe may further comprise a linker sequence of from 10-60 nucleotides.
8. Biochip
The present invention also relates to a biochip. The biochip may comprise a solid substrate comprising an attached probe or plurality of probes of the invention. The probes may be capable of hybridizing to a target sequence under stringent hybridization conditions. The probes may be attached at spatially defined address on the substrate. More than one probe per target sequence may be used, with either overlapping probes or probes to different sections of a particular target sequence. The probes may be capable of hybridizing to target sequences associated with a single disorder.
The probes may be attached to the biochip in a wide variety of ways, as will be appreciated by those in the art. The probes may either be synthesized first, with subsequent attachment to the biochip, or may be directly synthesized on the biochip.
The solid substrate may be a material that may be modified to contain discrete individual sites appropriate for the attachment or association of the probes and is amenable to at least one detection method. Representative examples of substrates include glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, TeflonJ, etc.), polysaccharides, nylon or nitrocellulose, resins, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses and plastics. The substrates may allow optical detection without appreciably fluorescing.
The substrate may be planar, although other configurations of substrates may be used as well. For example, probes may be placed on the inside surface of a tube, for flow-through sample analysis to minimize sample volume. Similarly, the substrate may be flexible, such as a flexible foam, including closed cell foams made of particular plastics.
The biochip and the probe may be derivatized with chemical functional groups for subsequent attachment of the two. For example, the biochip may be derivatized with a chemical functional group including, but not limited to, amino groups, carboxyl groups, oxo groups or thiol groups. Using these functional groups, the probes may be attached using functional groups on the probes either directly or indirectly using a linkers. The probes may be attached to the solid support by either the 5′ terminus, 3′ terminus, or via an internal nucleotide.
The probe may also be attached to the solid support non-covalently. For example, biotinylated oligonucleotides can be made, which may bind to surfaces covalently coated with streptavidin, resulting in attachment. Alternatively, probes may be synthesized on the surface using techniques such as photopolymerization and photolithography.
9. miRNA Expression Analysis
The present invention also relates to a method of identifying miRNAs that are associated with disease or a pathological condition comprising contacting a biological sample with a probe or biochip of the invention and detecting the amount of hybridization. PCR may be used to amplify nucleic acids in the sample, which may provide higher sensitivity.
The ability to identify miRNAs that are overexpressed or underexpressed in pathological cells compared to a control can provide high-resolution, high-sensitivity datasets which may be used in the areas of diagnostics, therapeutics, drug development, pharmacogenetics, biosensor development, and other related areas. An expression profile generated by the current methods may be a “fingerprint” of the state of the sample with respect to a number of miRNAs. While two states may have any particular miRNA similarly expressed, the evaluation of a number of miRNAs simultaneously allows the generation of a gene expression profile that is characteristic of the state of the cell. That is, normal tissue may be distinguished from diseased tissue. By comparing expression profiles of tissue in known different disease states, information regarding which miRNAs are associated in each of these states may be obtained. Then, diagnosis may be performed or confirmed to determine whether a tissue sample has the expression profile of normal or disease tissue. This may provide for molecular diagnosis of related conditions.
10. Determining Expression Levels
The present invention also relates to a method of determining the expression level of a disease-associated miRNA comprising contacting a biological sample with a probe or biochip of the invention and measuring the amount of hybridization. The expression level of a disease-associated miRNA is information in a number of ways. For example, a differential expression of a disease-associated miRNA compared to a control may be used as a diagnostic that a patient suffers from the disease. Expression levels of a disease-associated miRNA may also be used to monitor the treatment and disease state of a patient. Furthermore, expression levels of e disease-associated miRNA may allow the screening of drug candidates for altering a particular expression profile or suppressing an expression profile associated with disease.
A target nucleic acid may be detected by contacting a sample comprising the target nucleic acid with a biochip comprising an attached probe sufficiently complementary to the target nucleic acid and detecting hybridization to the probe above control levels.
The target nucleic acid may also be detected by immobilizing the nucleic acid to be examined on a solid support such as nylon membranes and hybridizing a labelled probe with the sample. Similarly, the target nucleic may also be detected by immobilizing the labeled probe to the solid support and hybridizing a sample comprising a labeled target nucleic acid. Following washing to remove the non-specific hybridization, the label may be detected.
The target nucleic acid may also be detected in situ by contacting permeabilized cells or tissue samples with a labeled probe to allow hybridization with the target nucleic acid. Following washing to remove the non-specifically bound probe, the label may be detected.
These assays can be direct hybridization assays or can comprise sandwich assays, which include the use of multiple probes, as is generally outlined in U.S. Pat. Nos. 5,681,702; 5,597,909; 5,545,730; 5,594,117; 5,591,584; 5,571,670; 5,580,731; 5,571,670; 5,591,584; 5,624,802; 5,635,352; 5,594,118; 5,359,100; 5,124,246; and 5,681,697, each of which is hereby incorporated by reference.
A variety of hybridization conditions may be used, including high, moderate and low stringency conditions as outlined above. The assays may be performed under stringency conditions which allow hybridization of the probe only to the target. Stringency can be controlled by altering a step parameter that is a thermodynamic variable, including, but not limited to, temperature, formamide concentration, salt concentration, chaotropic salt concentration pH, or organic solvent concentration.
Hybridization reactions may be accomplished in a variety of ways. Components of the reaction may be added simultaneously, or sequentially, in different orders. In addition, the reaction may include a variety of other reagents. These include salts, buffers, neutral proteins, e.g., albumin, detergents, etc. which may be used to facilitate optimal hybridization and detection, and/or reduce non-specific or background interactions. Reagents that otherwise improve the efficiency of the assay, such as protease inhibitors, nuclease inhibitors and anti-microbial agents may also be used as appropriate, depending on the sample preparation methods and purity of the target.
a. Diagnostic
The present invention also relates to a method of diagnosis comprising detecting a differential expression level of a disease-associated miRNA in a biological sample. The sample may be derived from a patient. Diagnosis of a disease state in a patient allows for prognosis and selection of therapeutic strategy. Further, the developmental stage of cells may be classified by determining temporarily expressed miRNA-molecules.
In situ hybridization of labeled probes to tissue arrays may be performed. When comparing the fingerprints between an individual and a standard, the skilled artisan can make a diagnosis, a prognosis, or a prediction based on the findings. It is further understood that the genes which indicate the diagnosis may differ from those which indicate the prognosis and molecular profiling of the condition of the cells may lead to distinctions between responsive or refractory conditions or may be predictive of outcomes.
b. Drug Screening
The present invention also relates to a method of screening therapeutics comprising contacting a pathological cell capable of expressing a disease related miRNA with a candidate therapeutic and evaluating the effect of a drug candidate on the expression profile of the disease associated miRNA. Having identified the differentially expressed miRNAs, a variety of assays may be executed. Test compounds may be screened for the ability to modulate gene expression of the disease associated miRNA. Modulation includes both an increase and a decrease in gene expression.
The test compound or drug candidate may be any molecule, e.g., protein, oligopeptide, small organic molecule, polysaccharide, polynucleotide, etc., to be tested for the capacity to directly or indirectly alter the disease phenotype or the expression of the disease associated miRNA. Drug candidates encompass numerous chemical classes, such as small organic molecules having a molecular weight of more than 100 and less than about 500, 1,000, 1,500, 2,000 or 2,500 daltons. Candidate compounds may comprise functional groups necessary for structural interaction with proteins, particularly hydrogen bonding, and typically include at least an amine, carbonyl, hydroxyl or carboxyl group, preferably at least two of the functional chemical groups. The candidate agents may comprise cyclical carbon or heterocyclic structures and/or aromatic or polyaromatic structures substituted with one or more of the above functional groups. Candidate agents are also found among biomolecules including peptides, saccharides, fatty acids, steroids, purines, pyrimidines, derivatives, structural analogs or combinations thereof.
Combinatorial libraries of potential modulators may be screened for the ability to bind to the disease associated miRNA or to modulate the activity thereof. The combinatorial library may be a collection of diverse chemical compounds generated by either chemical synthesis or biological synthesis by combining a number of chemical building blocks such as reagents. Preparation and screening of combinatorial chemical libraries is well known to those of skill in the art. Such combinatorial chemical libraries include, but are not limited to, peptide libraries encoded peptides, benzodiazepines, diversomers such as hydantoins, benzodiazepines and dipeptide, vinylogous polypeptides, analogous organic syntheses of small compound libraries, oligocarbamates, and/or peptidyl phosphonates, nucleic acid libraries, peptide nucleic acid libraries, antibody libraries, carbohydrate libraries, and small organic molecule libraries.
11. Gene Silencing
The present invention also relates to a method of using the nucleic acids of the invention to reduce expression of a target gene in a cell, tissue or organ. Expression of the target gene may be reduced by expressing a nucleic acid of the invention that comprises a sequence substantially complementary to one or more binding sites of the target mRNA. The nucleic acid may be a miRNA or a variant thereof. The nucleic acid may also be pri-miRNA, pre-miRNA, or a variant thereof, which may be processed to yield a miRNA. The expressed miRNA may hybridize to a substantially complementary binding site on the target mRNA, which may lead to activation of RISC-mediated gene silencing. An example for a study employing over-expression of miRNA is Yekta et al 2004, Science 304-594, which is incorporated herein by reference. One of ordinary skill in the art will recognize that the nucleic acids of the present invention may be used to inhibit expression of target genes using antisense methods well known in the art, as well as RNAi methods described in U.S. Pat. Nos. 6,506,559 and 6,573,099, which are incorporated by reference.
The target of gene silencing may be a protein that causes the silencing of a second protein. By repressing expression of the target gene, expression of the second protein may be increased. Examples for efficient suppression of miRNA expression are the studies by Esau et al 2004 JBC 275-52361; and Cheng et al 2005 Nucleic Acids Res. 33-1290, which is incorporated herein by reference.
12. Gene Enhancement
The present invention also relates to a method of using the nucleic acids of the invention to increase expression of a target gene in a cell, tissue or organ. Expression of the target gene may be increased by expressing a nucleic acid of the invention that comprises a sequence substantially complementary to a pri-miRNA, pre-miRNA, miRNA or a variant thereof. The nucleic acid may be an anti-miRNA. The anti-miRNA may hybridize with a pri-miRNA, pre-miRNA or miRNA, thereby reducing its gene repression activity. Expression of the target gene may also be increased by expressing a nucleic acid of the invention that is substantially complementary to a portion of the binding site in the target gene, such that binding of the nucleic acid to the binding site may prevent miRNA binding.
13. Therapeutic
The present invention also relates to a method of using the nucleic acids of the invention as modulators or targets of disease or disorders associated with developmental dysfunctions, such as cancer. In general, the claimed nucleic acid molecules may be used as a modulator of the expression of genes which are at least partially complementary to said nucleic acid. Further, miRNA molecules may act as target for therapeutic screening procedures, e.g. inhibition or activation of miRNA molecules might modulate a cellular differentiation process, e.g. apoptosis.
Furthermore, existing miRNA molecules may be used as starting materials for the manufacture of sequence-modified miRNA molecules, in order to modify the target-specificity thereof, e.g. an oncogene, a multidrug-resistance gene or another therapeutic target gene. Further, miRNA molecules can be modified, in order that they are processed and then generated as double-stranded siRNAs which are again directed against therapeutically relevant targets. Furthermore, miRNA molecules may be used for tissue reprogramming procedures, e.g. a differentiated cell line might be transformed by expression of miRNA molecules into a different cell type or a stem cell.
14. Compositions
The present invention also relates to a pharmaceutical composition comprising the nucleic acids of the invention and optionally a pharmaceutically acceptable carrier. The compositions may be used for diagnostic or therapeutic applications. The administration of the pharmaceutical composition may be carried out by known methods, wherein a nucleic acid is introduced into a desired target cell in vitro or in vivo. Commonly used gene transfer techniques include calcium phosphate, DEAE-dextran, electroporation, microinjection, viral methods and cationic liposomes.
15. Kits
The present invention also relates to kits comprising a nucleic acid of the invention together with any or all of the following: assay reagents, buffers, probes and/or primers, and sterile saline or another pharmaceutically acceptable emulsion and suspension base. In addition, the kits may include instructional materials containing directions (e.g., protocols) for the practice of the methods of this invention.
EXAMPLE 1
Prediction of MiRNAs
We surveyed the entire human genome for potential miRNA coding genes using two computational approaches similar to those described in U.S. Patent Application No. 60/522,459, Ser. No. 10/709,577 and Ser. No. 10/709,572, the contents of which are incorporated herein by reference, for predicting miRNAs. Briefly, non-protein coding regions of the entire human genome were scanned for hairpin structures. The predicted hairpins and potential miRNAs were scored by thermodynamic stability, as well as structural and contextual features. The algorithm was calibrated by using miRNAs in the Sanger Database which had been validated.
1. First Screen
The first screen was described in U.S. patent application Ser. No. 10/709,572, in which Table 2 shows the sequence (“PRECURSOR SEQUENCE”), sequence identifier (“PRECUR SEQ-ID”) and organism of origin (“GAM ORGANISM”) for each predicted hairpin from the first computational screen, together with the predicted miRNAs (“GAM NAME”). Table 1 of U.S. patent application Ser. No. 10/709,572, the contents of which are incorporated herein by reference, shows the sequence (“GAM RNA SEQUENCE”) and sequence identifier (“GAM SEQ-ID”) for each miRNA (“GAM NAME”), along with the organism of origin (“GAM ORGANISM”) and Dicer cut location (“GAM POS”). The sequences of the predicted hairpins and miRNA are also set forth in the Sequence Listing of U.S. patent application Ser. No. 10/709,572, the contents of which are incorporated herein by reference.
2. Second Screen
Table 1 lists the numerical identifier for each predicted hairpin (“HID”) of the second computational screen. Table 1 also lists the genomic location for each hairpin (“Hairpin Location”). The format for the genomic location is a concatenation of <chr_id><strand><start position>. For example, 19+135460000 refers chromosome 19, +strand, start position 135460000. Chromosomes 23-25 refer to chromosome X, chromosome Y and mitochondrial DNA. The chromosomal location is based on the hg17 assembly of the human genome by UCSC (genome.ucsc.edu), which is based on NCBI Build 35 version 1 and was produced by the International Human Genome Sequencing Consortium.
Table 1 also lists whether the hairpin is conserved in evolution (“C”). There is an option that there is a paper of the genome version. The hairpins were identified as conserved (“Y”) or nonconserved (“N”) by using phastCons data. The phastCons data is a measure of evolutionary conservation for each nucleotide in the human genome against the genomes of chimp, mouse, rat, dog, chicken, frog, and zebrafish, based on a phylo-HMM using best-in-genome pair wise alignment for each species based on BlastZ, followed by multiZ alignment of the 8 genomes (Siepel et al, J. Comput. Biol 11, 413-428, 2004 and Schwartz et al., Genome Res. 13, 103-107, 2003). A hairpin is listed as conserved if the average phastCons conservation score over the 7 species in any 15 nucleotide sequence within the hairpin stem is at least 0.9 (Berezikov, E. et al. Phylogenetic Shadowing and Computational Identification of Human microRNA Genes. Cell 120, 21-24, 2005).
Table 1 also lists the genomic type for each hairpin (“T”) as either intergenic (“G”), intron (“I”) or exon (“E”). Table 1 also lists the numerical identifier (“MID”) for each predicted miRNA and miRNA*. Table 1 also lists the prediction score grade for each hairpin (“P”) on a scale of 0-1 (1 the hairpin is the most reliable), as described in Hofacker et al., Monatshefte f. Chemie 125: 167-188, 1994. If the grade is zero or null, they are transformed to the lower value of PalGrade that its p-value is <0.05. Table 1 also lists the p-value (“Pval”) calculated out of background hairpins for the values of each P scores. As shown in Table, there are few instances where the Pval is >0.05. In each of these cases, the hairpins are highly conserved or they have been validated (F=Y).
Table 1 also lists whether the miRNAs were validated by expression analysis (“E”) (Y=Yes, N=No), as detailed in Table 2. Table 1 also lists whether the miRNAs were validated by sequencing (“S”) (Y=Yes, N=No). If there was a difference in sequences between the predicted and sequenced miRNAs, the sequenced sequence is predicted. It should be noted that failure to sequence or detect expression of a miRNA does not necessarily mean that a miRNA does not exist. Such undetected miRNAs may be expressed in tissues other than those tested. In addition, such undetected miRNAs may be expressed in the test tissues, but at a difference stage or under different condition than those of the experimental cells.
Table 1 also listed whether the miRNAs were shown to be differentially expressed (“D”) (Y=Yes, N=No) in at least one disease, as detailed in Table 2). Table 1 also whether the miRNAs were present (“F”) (Y=Yes, N=No) in Sanger DB Release 6.0 (April 2005) (http://nar.oupjournals.org/) as being detected in humans or mice or predicted in humans. As discussed above, the miRNAs listed in the Sanger database are a component of the prediction algorithm and a control for the output.
Table 1 also lists a genetic location cluster (“LC”) for those hairpins that are within 5,000 nucleotides of each other. Each miRNA that has the same LC share the same genetic cluster. Table 1 also lists a seed cluster (“SC”) to group miRNAs by their seed of 2-7 by an exact match. Each miRNA that has the same SC have the same seed. For a discussion of seed lengths of 5 nucleotides, see Lewis et al., Cell, 120; 15-20 (2005).
EXAMPLE 2
Prediction of Target Genes
The predicted miRNAs from the two computational screens of Example 1 were then used to predict target genes and their binding sites using two computational approaches similar to those described in U.S. Patent Application No. 60/522,459, Ser. No. 10/709,577 and Ser. No. 10/709,572, the contents of which are incorporated herein by reference, for predicting miRNAs.
1. First Screen
Table 6 of U.S. patent application Ser. No. 10/709,572, the contents of which are incorporated herein by reference, lists the predicted target genes (“TARGET”) and binding site sequence (“TARGET BINDING SITE SEQUENCE”) and binding site sequence identifier (“TARGET BINDING SITE SEQ-ID”) from the first computational screen, as well as the organism of origin for the target (“TARGET ORGANISM”). Table 12 of U.S. patent application Ser. No. 10/709,572, the contents of which are incorporated herein by reference, lists the diseases (“DISEASE NAME”) that are associated with the target genes (“TARGET-GENES ASSOCIATED WITH DISEASE”). Table 14 of U.S. patent application Ser. No. 10/709,572, the contents of which are incorporated herein by reference, lists the sequence identifiers for the miRNAs (“SEQ ID NOs OF GAMS ASSOCIATED WITH DISEASE”) and the diseases (“DISEASE NAME”) that are associated with the miRNA based on the target gene. The sequences of the binding site sequences are also set forth on the Sequence Listing of U.S. patent application Ser. No. 10/709,572, the contents of which are incorporated herein by reference.
2. Second Screen
Table 4 lists the predicted target gene for each miRNA (MID) and its hairpin (HID) from the second computational screen. The names of the target genes were taken from NCBI Reference Sequence release 9 (www.ncbi.nlm.nih.gov; Pruitt et al., Nucleic Acids Res, 33(1):D501-D504, 2005; Pruitt et al., Trends Genet., 16(1):44-47, 2000; and Tatusova et al., Bioinformatics, 15(7-8):536-43, 1999). Target genes were identified by having a perfect complimentary match of a 7 nucleotide miRNA seed (positions 2-8) and an A on the UTR (total=8 nucleotides). For a discussion on identifying target genes, see Lewis et al., Cell, 120: 15-20, (2005). For a discussion of the seed being sufficient for binding of a miRNA to a UTR, see Lim Lau et al., (Nature 2005) and Brenneck et al, (PLoS Biol 2005).
Binding sites were then predicted using a filtered target genes dataset by including only those target genes that contained a UTR of a least 30 nucleotides. The binding site screen only considered the first 4000 nucleotides per UTR and considered the longest transcript when there were several transcripts per gene. The filtering reduced the total number of transcripts from 23626 to 14239. Table 4 lists the SEQ ID NO for the predicted binding sites for each target gene, as described in the Sequence Listing of International Publication WO 2005/111211, the contents of which are incorporated herein by reference. The sequence of the binding site includes the 20 nucleotides 5′ and 3′ of the binding site as they are located on the spliced mRNA. Except for those miRNAs that have only a single predicted binding site or those miRNAs that were validated, the data in Table 4 has been filtered to only indicate those target genes with at least 2 binding sites.
Table 5 shows the relationship between the miRNAs (“MID”)/hairpins (“HID”) and diseases by their target genes. The name of diseases are taken from OMIM. For a discussion of the rational for connecting the host gene the hairpin is located upon to disease, see Baskerville and Bartel, RNA, 11: 241-247 (2005) and Rodriguez et al., Genome Res., 14: 1902-1910 (2004). Table 5 shows the number of miRNA target genes (“N”) that are related to the disease. Table 5 also shows the total number of genes that are related to the disease (“T”), which is taken from the genes that were predicted to have binding sites for miRNAs. Table 5 also shows the percentage of N out of T and the p-value of hypergeometric analysis (“Pval”). Table 8 shows the disease codes for Tables 5 and 6. For a reference of hypergeometric analysis, see Schaum's Outline of Elements of Statistics II: Inferential Statistics.
Table 6 shows the relationship between the miRNAs (“MID”)/hairpins (“HID”) and diseases by their host genes. We defined hairpins genes on the complementary strand of a host gene as located on the gene: Intron_c as Interon and Exon_c as Exon. We choose the complementary strands as they can cause disease. For example, a mutation in the miRNA that is located on the complementary strand. In those case that a miRNA in on both strands, two statuses like when Intron and Exon_c Intron is the one chosen. The logic of choosing is Intron>Exon>Intron_c>Exon_c>Intergenic. Table 9 shows the relationship between the target sequences (“Gene Name”) and disease (“Disease Code”).
EXAMPLE 3
Validation of miRNAs
1. Expression Analysis—Set 1
To confirm the hairpins and miRNAs predicted in Example 1, we detected expression in various tissues using the high-throughput microarrays similar to those described in U.S. Patent Application No. 60/522,459, Ser. No. 10/709,577 and Ser. No. 10/709,572, the contents of which are incorporated herein by reference. For each predicted precursor miRNA, mature miRNAs derived from both stems of the hairpin were tested.
Table 2 shows the hairpins (“HID”) of the second prediction set that were validated by detecting expression of related miRNAs (“MID”), as well as a code for the tissue (“Tissue”) that expression was detected. The tissue and diseases codes for Table 2 are listed in Table 7. Some of the tested tissues wee cell line. Lung carcinoma cell line (H1299) with/without P53: H1299 has a mutated P53. The cell line was transfected with a construct with P53 that is temperature sensitive (active at 32° C.). The experiment was conducted at 32° C.
Table 2 also shows the chip expression score grade (range of 500-65000). A threshold of 500 was used to eliminate non-significant signals and the score was normalized by MirChip probe signals from different experiments. Variations in the intensities of fluorescence material between experiments may be due to variability in RNA preparation or labeling efficiency. We normalized based on the assumption that the total amount of miRNAs in each sample is relatively constant. First we subtracted the background signal from the raw signal of each probe, where the background signal is defined as 400. Next, we divided each miRNA probe signal by the average signal of all miRNAs, multiplied the result by 10000 and added back the background signal of 400. Thus, by definition, the sum of all miRNA probe signals in each experiment is 10400.
Table 2 also shows a statistical analysis of the normalized signal (“Spval”) calculated on the normalized score. For each miRNA, we used a relevant control group out of the full predicted miRNA list. Each miRNA has an internal control of probes with mismatches. The relevant control group contained probes with similar C and G percentage (abs diff <5%) in order to have similar Tm. The probe signal P value is the ratio over the relevant control group probes with the same or higher signals. The results are p-value ≦0.05 and score is above 500. In those cases that the SPVal is listed as 0.0, the value is less than 0.0001.
2. Expression Analysis—Set 2
To further confirm the hairpins and miRNAs predicted in Example 1, we detected expression in additional tissues. Table 2 of U.S. Provisional Patent Application No. 60/655,094, the contents of which are incorporated herein by reference, lists expression data of miRNAs by the following: HID: hairpin sequence identifier for sequence set forth in the Sequence Listings of U.S. Provisional Patent Application No. 60/655,094, the contents of which are incorporated herein by reference; MID: miRNA sequence identifier for sequence set forth in the Sequence Listings of U.S. Provisional Patent Application No. 60/655,094, the contents of which are incorporated herein by reference; Tissue: tested tissue; S: chip expression score grade (range=100-65000); Dis. Diff. Exp.: disease related differential expression and the tissue it was tested in; R: ratio of disease related expression (range=0.01-99.99); and abbreviations: Brain Mix A—a mixture of brain tissue that are affected in Alzheimer; Brain Mix B—a mixture of all brain tissues; and Brain SN—Substantia Nigra.
3. Sequencing
To further validate the hairpins (“HID”) of the second prediction, a number of miRNAs were validated by sequencing methods similar to those described in U.S. Patent Application No. 60/522,459, Ser. No. 10/709,577 and Ser. No. 10/709,572, the contents of which are incorporated herein by reference. Table 3 shows the hairpins (“HID”) that were validated by sequencing a miRNA (MID) in the indicated tissue (“Tissue”).
EXAMPLE 4
MiRNAs of Chromosome 19
A group of the validated miRNAs from Example 3 were highly expressed in placenta, have distinct sequence similarity, and are located in the same locus on chromosome 19 (FIG. 2A-2B). These predicted miRNAs are spread along a region of  ̃100,000 nucleotides in the 19q13.42 locus. This genomic region is devoid of protein-coding genes and seems to be intergenic. Further analysis of the genomic sequence, including a thorough examination of the output of our prediction algorithm, revealed many more putative related miRNAs, and located mir-371, mir-372, and mir-373 approximately 25,000 bp downstream to this region. Overall, 54 putative miRNA precursors were identified in this region. The miRNA precursors can be divided into four distinct types of related sequences (FIGS. 2A-2B). About 75% of the miRNAs in the cluster are highly related and were labeled as type A. Three other miRNA types, types B, C and D, are composed of 4, 2, and 2 precursors, respectively. An additional 3 putative miRNA precursors (S1 to S3) have unrelated sequences. Interestingly, all miRNA precursors are in the same orientation as the neighboring mir-371, mir-372, and mir-373 miRNA precursors.
Further sequence analysis revealed that the majority of the A-type miRNAs are embedded in a  ̃600 bp region that is repeated 35 times in the cluster. The repeated sequence does not appear in other regions of the genome and is conserved only in primates. The repeating unit is almost always bounded by upstream and downstream Alu repeats. This is in sharp contrast to the MC14-1 cluster which is extremely poor in Alu repeats.
FIG. 3A shows a comparison of sequences of the 35 repeat units containing the A-type miRNA precursors in human. The comparison identified two regions exhibiting the highest sequence similarity. One region includes the A-type miRNA, located in the 3′ region of the repeat. The second region is located  ̃100 nucleotides upstream to the A-type miRNA precursors. However, the second region does not show high similarity among the chimp repeat units while the region containing the A-type miRNA precursors does (FIG. 3B).
Examination of the region containing the A-type repeats showed that the 5′ region of the miRNAs encoded by the 5′ stem of the precursors (5p miRNAs) seem to be more variable than other regions of the mature miRNAs. This is matched by variability in the 3′ region of the mature miRNAs derived from the 3′ stems (3p miRNAs). As expected, the loop region is highly variable. The same phenomenon can also be observed in the multiple sequence alignment of all 43 A-type miRNAs (FIGS. 4A-4C).
The multiple sequence alignment presented in FIGS. 4A-4C revealed the following findings with regards to the predicted mature miRNAs. The 5p miRNAs can be divided into 3 blocks. Nucleotides 1 to 6 are C/T rich, relatively variable, and are marked in most miRNAs by a CTC motif in nucleotides 3 to 5. Nucleotides 7 to 15 are A/G rich and apart from nucleotides 7 and 8 are shared among most of the miRNAs. Nucleotides 16 to 23 are C/T rich and are, again, conserved among the members. The predicted 3p miRNAs, in general, show a higher conservation among the family members. Most start with an AAA motif, but a few have a different 5′ sequence that may be critical in their target recognition. Nucleotides 8 to 15 are C/T rich and show high conservation. The last 7 nucleotides are somewhat less conserved but include a GAG motif in nucleotides 17 to 19 that is common to most members.
Analysis of the 5′ region of the repeated units identified potential hairpins. However, in most repeating units these hairpins were not preserved and efforts to clone miRNAs from the highest scoring hairpins failed. There are 8 A-type precursors that are not found within a long repeating unit. Sequences surrounding these precursors show no similarity to the A-type repeating units or to any other genomic sequence. For 5 of these A-type precursors there are Alu repeats located significantly closer downstream to the A-type sequence.
The other miRNA types in the cluster showed the following characteristics. The four B group miRNAs are found in a repeated region of  ̃500 bp, one of which is located at the end of the cluster. The two D-type miRNAs, which are  ̃2000 nucleotides from each other, are located at the beginning of the cluster and are included in a duplicated region of 1220 nucleotides. Interestingly, the two D-type precursors are identical. Two of the three miRNAs of unrelated sequence, S1 and S2, are located just after the two D-type miRNAs, and the third is located between A34 and A35. In general, the entire  ̃100,000 nucleotide region containing the cluster is covered with repeating elements. This includes the miRNA-containing repeating units that are specific to this region and the genome wide repeat elements that are spread in the cluster in large numbers.
EXAMPLE 5
Cloning of Predicted MiRNAs
To further validate the predicted miRNAs, a number of the miRNAs described in Example 4 were cloned using methods similar to those described in U.S. Patent Application No. 60/522,459, Ser. No. 10/709,577 and Ser. No. 10/709,572, the contents of which are incorporated herein by reference. Briefly, a specific capture oligonucleotide was designed for each of the predicted miRNAs. The oligonucleotide was used to capture, clone, and sequence the specific miRNA from a placenta-derived library enriched for small RNAs.
We cloned 41 of the 43 A-type miRNAs, of which 13 miRNAs were not present on the original microarray but only computationally predicted, as well as the D-type miRNAs. For 11 of the predicted miRNA precursors, both 5p and 3p predicted mature miRNAs were present on the microarray and in all cases both gave significant signals. Thus, we attempted to clone both 5′ and 3′ mature miRNAs in all cloning attempts. For 27 of the 43 cloned miRNA, we were able to clone miRNA derived from both 5′ and 3′ stems. Since our cloning efforts were not exhaustive, it is possible that more of the miRNA precursors encode both 5′ and 3′ mature miRNAs.
Many of the cloned miRNAs have shown heterogeneity at the 3′ end as observed in many miRNA cloning studies (Lagos-Quintana 2001, 2002, 2003) (Poy 2004). Interestingly, we also observed heterogeneity at the 5′ end for a significant number of the cloned miRNAs. This heterogeneity seemed to be somewhat more prevalent in 5′-stem derived miRNAs (9) compared to 3′-stem derived miRNAs (6). In comparison, heterogeneity at the 3′ end was similar for both 3′ and 5′-stem derived miRNAs (19 and 13, respectively). The 5′ heterogeneity involved mainly addition of one nucleotide, mostly C or A, but in one case there was an addition of 3 nucleotides. This phenomenon is not specific to the miRNAs in the chromosome 19 cluster. We have observed it for many additional cloned miRNAs, including both known miRNAs as well as novel miRNAs from other chromosomes (data not shown).
EXAMPLE 6
Analysis of MiRNA Expression
To further examine the expression of the miRNAs of Example 4, we used Northern blot analysis to profile miRNA expression in several tissues. Northern blot analysis was performed using 40 μg of total RNA separated on 13% denaturing polyacrylamide gels and using 32P end labeled oligonucleotide probes. The oligonucleotide probe sequences were 5′ ACTCTAAAGAGAAGCGCTTTGT-3′ (SEQ ID NO: 5) (A19-3p, NCBI: HSA-MIR-RG-21) and 5′ ACCCACCAAAGAGAAGCACTTT-3′ (SEQ ID NO:6) (A24-3p, NCBI: HSA-MIR-RG-27). The miRNAs were expressed as  ̃22 nucleotide long RNA molecules with tissue specificity profile identical to that observed in the microarray analysis (FIG. 5A).
In order to determine how the MC19-1 cluster is transcribed. A survey of the ESTs in the region identified only one place that included ESTs with poly-adenylation signal and poly-A tail. This region is located just downstream to the A43 precursor. The only other region that had ESTs with poly-adenylation signal is located just after mir-373, suggesting that mir-371,2,3 are on a separate transcript. We performed initial studies focusing on the region around mir-A43 to ensure that the region is indeed transcribed into poly-adenylated mRNA. RT-PCR experiments using primers covering a region of 3.5 kb resulted in obtaining the expected fragment (FIG. 5B). RT-PCR analysis was performed using 5 μg of placenta total RNA using oligo-dT as primer. The following primers were used to amplify the transcripts:









(SEQ ID NO: 7)



f1: 5′-GTCCCTGTACTGGAACTTGAG-3′;


 



(SEQ ID NO: 8)



f2: 5′-GTGTCCCTGTACTGGAACGCA-3′;


 



(SEQ ID NO: 9)



r1: 5′-GCCTGGCCATGTCAGCTACG-3′;


 



(SEQ ID NO: 10)



r2: 5′-TTGATGGGAGGCTAGTGTTTC-3′;


 



(SEQ ID NO: 11)



r3: 5′ GACGTGGAGGCGTTCTTAGTC-3′; 



and


 



(SEQ ID NO: 12)



r4: 5′-TGACAACCGTTGGGGATTAC-3′.






The authenticity of the fragment was validated by sequencing. This region includes mir-A42 and mir-A43, which shows that both miRNAs are present on the same primary transcript.
Further information on the transcription of the cluster came from analysis of the 77 ESTs located within it. We found that 42 of the ESTs were derived from placenta. As these ESTs are spread along the entire cluster, it suggested that the entire cluster is expressed in placenta. This observation is in-line with the expression profile observed in the microarray analysis. Thus, all miRNAs in the cluster may be co-expressed, with the only exception being the D-type miRNAs which are the only miRNAs to be expressed in HeLa cells. Interestingly, none of the 77 ESTs located in the region overlap the miRNA precursors in the cluster. This is in-line with the depletion of EST representation from transcripts processed by Drosha.
Examination of the microarray expression profile revealed that miRNAs D1/2, A12, A21, A22, and A34, have a somewhat different expression profile reflected as low to medium expression levels in several of the other tissues examined. This may be explained by alternative splicing of the transcript(s) encoding the miRNAs or by the presence of additional promoter(s) of different tissues specificity along the cluster.
Comparison of the expression of 3p and 5p mature miRNAs revealed that both are expressed for many miRNA precursors but in most cases at different levels. For most pre-miRNAs the 3p miRNAs are expressed at higher levels then the 5p miRNAs. However, in 6 cases (mir-D1,2, mir-A1, mir-A8, mir-A12, mir-A17 and mir-A33) both 3p and 5p miRNAs were expressed at a similar level, and in one case (mir-A32) the 5p miRNA was expressed at higher levels then the 3p miRNA.
EXAMPLE 7
Conservation
Comparison of the sequences from all four types of predicted miRNAs of Example 4 to that of other species (chimp, macaque, dog, chicken, mouse, rat, drosophila, zebra-fish, fungi, c. elegans) revealed that all miRNAs in the cluster, and in fact the entire region, are not conserved beyond primates. Interestingly, homologues of this region do not exist in any other genomes examined, including mouse and rat. Thus, this is the first miRNA cluster that is specific to primates and not generally shared in mammals. Homology analysis between chimp and human show that all 35 repeats carrying the A-type miRNAs are contiguous between the two species. Furthermore, the entire cluster seems to be identical between human and chimp. Thus, the multiple duplications leading to the emergence of the MC19-1 cluster must have occurred prior to the split of chimp and human and remained stable during the evolution of each species. It should be noted that human chromosome 19 is known to include many tandemly clustered gene families and large segmental duplications (Grimwood et al, 2004). Thus, in this respect the MC19-1 cluster is a natural part of chromosome 19.
In comparison, the MC14-1 cluster is generally conserved in mouse and includes only the A7 and A8 miRNAs within the cluster are not conserved beyond primates (Seitz 2004). In contrast all miRNAs in the MC19-1 cluster are unique to primates. A survey of all miRNAs found in Sanger revealed that only three miRNA, mir-198, mir-373, and mir-422a, are not conserved in the mouse or rat genomes, however, they are conserved in the dog genome and are thus not specific to primates. Interestingly, mir-371 and mir-372, which are clustered with mir-373, and are located 25 kb downstream to the MC19-1 cluster, are homologous to some extent to the A-type miRNAs (FIGS. 4A-4C), but are conserved in rodents.
Comparison of the A-type miRNA sequences to the miRNAs in the Sanger database revealed the greatest homology to the human mir-302 family (FIG. 4C). This homology is higher than the homology observed with mir-371,2,3. The mir-302 family (mir-302a, b, c, and d) are found in a tightly packed cluster of five miRNAs (including mir-367) covering 690 nucleotides located in the antisense orientation in the first intron within the protein coding exons of the HDCMA18P gene (accession NM_016648). No additional homology, apart from the miRNA homology, exists between the mir-302 cluster and the MC19-1 cluster. The fact that both the mir-371,2,3 and mir-302a,b,c,d are specific to embryonic stem cells is noteworthy.
EXAMPLE 8
Differential Expression of miRNAs
Using chip expression methods similar to those described in 0, microarray images were analyzed using Feature Extraction Software (Version 7.1.1, Agilent). Table 2 shows the ratio of disease related expression (“R”) compared to normal tissues. Table 2 also shows the statistical analysis of the normalized signal (“RPval”). The signal of each probe was set as its median intensity. Signal intensities range from background level of 400 to saturating level of 66000. 2 channels hybridization was performed and Cy3 signals were compared to Cy5 signals, where fluor reversed chip was preformed (normal vs. disease), probe signal was set to be its average signal. Signals were normalized by dividing them with the known miRNAs average signals such that the sum of known miRNAs signal is the same in each experiment or channel. Signal ratios between disease and normal tissues were calculated. Signal ratio greater than 1.5 indicates a significant upregulation with a P value of 0.007 and signal ratio greater than 2 has P value of 0.003. P values were estimated based on the occurrences of such or greater signal ratios over duplicated experiments.
The differential expression analysis in Table 2 indicates that the expression of a number of the miRNAs are significantly altered in disease tissue. In particular, the MC19-1 miRNAs of Example 4 are differentially expressed in prostate and lung cancer. The relevance of the MC19-1 miRNAs to cancer is supported by the identification of a loss of heterozygosity within the MC19-1 region in prostate cancer derived cells (Dumur et al. 2003).







TABLE 1







HAIRPINS AND MICRORNAS



















HID
Hairpin Loc
C
T
MID
P
Pval
E
S
D
F
LC
SC






















778
3+44130716
Y
G
8545
0.46
0.0101
Y
N
Y
Y

1154


778
3+44130716
Y
G
8546
0.46
0.0101
N
N
N
N

1155


778
3+44130716
Y
G
8547
0.46
0.0101
N
Y
N
N

6
















TABLE 2







EXPRESSION AND DIFFERENTIAL EXPRESSION


IN DISEASES OF MICRORNAS














HID
MID
Tissue
S
SPval
Disease
R
RPval

















778
8545
10
589
0.0104 





778
8545
11
91177
0 





778
8545
7
6175
0





778
8545
9
957
0.0052





778
8545
13
7047
0





778
8545
12
1813
0.0078





778
8545
5
936
0.007





778
8545



1
1.62
0.0068


778
8545



2
0.43
0.0053


778
8545
10
627
0.0078 





778
8545
11
205621
0





778
8545
7
6818
0





778
8545
9
1029
0.0035





778
8545
13
7911
0





778
8545
12
2091
0.0078





778
8545
5
1019
0.0052





778
8545



1
1.64
0.0067


778
8545



2
0.39
0.005 


778
8545
10
589
0.0104





778
8545
7
6175
0





778
8545
9
957
0.0052





778
8545
13
7047
0





778
8545
12
1813
0.0078 





778
8545
5
936
0.007





778
8545



1
1.62
0.0068


778
8545



2
0.43
0.0053
















TABLE 3







SEQUENCED MICRORNAS









HID
MID
Tissue





778
8547
11
















TABLE 4







TARGET GENES AND BINDING SITES









HID
MID
Target Genes and Binding Sites





778
8545
ARL10B (109601, 109602); ARNT2 (109611, 109612); CCT5 (109603, 109604);




DIRAS1 (109622, 109623); EPHA8 (109599, 109600); GPR124 (109605, 109606, 




109607); IXL (109620, 109621); NFIX (109617, 109618, 109619); PCOLN3




(109613, 109614); RARA (109615, 109616); SYT13 (109608, 109609, 109610);


778
8546
C2orf26 (109628, 109629); CHML (109626, 109627); DGKI (109632, 109633);




EFCBP1 (109634, 109635); EFNB3 (109636, 109637); FLJ20160 (109630, 




109631); HRNR (109624, 109625);


778
8547
13CDNA73 (109805); AASDHPPT (109783); ABCA6 (109844); ABI1 (109774);




ACACA (109840); ADARB1 (109863); ADCY2 (109718); AEBP2 (109792); ALS2CR3




(109679); ANKH (109724); ANP32E (109653); AP1G1 (109830); ARHGAP18




(109743); ARL6IP5 (109688); ATOH7 (109777); ATP11A (109808); ATP11C




(109876); ATP2B3 (109871); ATXN10 (109865); BBS5 (109669); BCL2L14




(109791); BID (109866); BLP1 (109754); BRPF3 (109733); BRUNOL6 (109823);




C10orf26 (109770); C12orf22 (109799); C13orf25 (109806); C1orf21




(109647); C20orf7 (109859); C6orf198 (109744); C9orf28 (109760); CCND2




(109790); CCPG1 (109822); CD22 (109851); CD2AP (109735); CD80 (109700);




CDC2L6 (109740); CDCA5 (109787); CDH13 (109827); CHRFAM7A (109821); CIR




(109678); CLEC1A (109798); CNTNAP5 (109667); COL4A6 (109873); COMMD3




(109764); CRI2 (109855); CRISPLD2 (109828); CSPG3 (109849); CTSS




(109654); CYP3A7 (109750); CYP4F3 (109848); DDAH2 (109739); DDX19L




(109826); DDX3Y (109877); DHFR (109725); DKFZp564J157 (109794); DKK2




(109714); DLEU7 (109809); DMXL1 (109720); DPP9 (109854); DUSP3 (109842); 




DYM (109847); E2F7 (109802); E2IG5 (109689); EAF1 (109682); ECHDC1




(109742); EFHA2 (109751); ENPEP (109707); EPB41L1 (109860); ERBB4




(109680); ESCO1 (109846); FAHD1 (109824); FARP2 (109674); FCHSD1




(109728); FCRL2 (109645); FIP1L1 (109704); FLJ35775 (109755); FPRL2




(109852); FSTL5 (109716); FXC1 (109779); GCET2 (109698); GDAP1L1




(109861); GDF6 (109757); GHR (109719); GMFB (109814); GNPNAT1 (109813); 




GORASP1 (109694); GOSR1 (109833); GP5 (109703); GPC3 (109875); GREM2




(109658); HAN11 (109836); HECA (109736); HLCS (109864); HPS3 (109691);




HRB (109673); HS2ST1 (109643); HSXIAPAF1 (109832); hSyn (109796); IHPK1




(109696); IL8RB (109672); INA (109771); ING1 (109807); IQCC (109639);




IRF4 (109732); ISGF3G (109810); ISLR (109818); IVD (109817); JAGN1




(109681); JMJD1C (109776); KA36 (109841); KAB (109659); KCNJ2 (109837);




KIAA0478 (109638); KIAA0553 (109843); KIAA1078 (109648); KIAA1463




(109793); KIAA1609 (109831); KIAA1712 (109709); KIAA1729 (109711); KIT




(109705); KLHL4 (109870); KLHL8 (109712); LDB3 (109768); LOC340156




(109737); LPXN (109786); LRP2BP (109717); LRPPRC (109676); LRRTM2




(109727); LUZP1 (109651); MAGEB4 (109869); MAGEB6 (109868); MAK3




(109699); MARVELD1 (109769); MEGF10 (109722); MGC51082 (109856); MLLT2




(109706); MOBKL2B (109763); MRFAP1L1 (109710); MXI1 (109772); MYO1D




(109839); MYST2 (109834); NAP1L1 (109801); NAP1L5 (109713); NARG1




(109708); NAV1 (109649); NBS1 (109756); NCKIPSD (109695); NEU3 (109781); 




NFX1 (109759); NIN (109812); NIPA1 (109819, 109820); NKTR (109685, 




109686); NMNAT2 (109655); NSUN4 (109640); NUDT13 (109767); NUDT16




(109690); OXSR1 (109684); P2RY1 (109692); PAK7 (109862); PCAF (109683);




PDE10A (109745); PDE5A (109715); PDE6A (109729); PDK1 (109670); PDPR




(109825); PHF20L1 (109753); PHYHIPL (109766); PLAA (109762); PLCB1




(109858); PLEKHK1 (109775); POLQ (109701); POMZP3 (109748); PRKCE




(109661); PRKG1 (109765); PRSS23 (109782); PSD4 (109665); PTGFR




(109642); PTPN11 (109797); RAB3GAP (109668); RAB4A (109650); RAB6A




(109788); RALB (109666); RALGPS1 (109761); RANBP9 (109738); RAP2B




(109693); RASGRP3 (109660); RIOK3 (109845); RIPK5 (109657); RPIA




(109662); SAMD12 (109758); SAMD9 (109749); SEPT6 (109874); SFRS11




(109641); SFXN5 (109677); SGCD (109723); SLC25A16 (109778); SLC25A27




(109734); SLC36A2 (109730); SLC5A7 (109664); SLICK (109656); SLITRK3




(109702); SMC1L1 (109872); SMC6L1 (109675); SNX24 (109721); SPARC




(109731); SPOCK (109726); SPRED1 (109816); STAT2 (109800); STXBP4




(109835); TBC1D15 (109795); TBRG1 (109784); TDE2 (109741); THUMPD1




(109829); TMCC3 (109803); TRAPPC6B (109811); TRIM68 (109785); TUBAL3




(109773); TUFT1 (109644); UCP3 (109789); UHMK1 (109646); UNC5D (109752);




VGL-3 (109697); WARS2 (109652); XBP1 (109867); ZAK (109671); ZFYVE1




(109815); ZNF160 (109857); ZNF2 (109663); ZNF215 (109780); ZNF507




(109850); ZNF528 (109853); ZNF588 (109746); ZNF605 (109804); ZNF624




(109838); ZNF660 (109687); ZNF92 (109747);

































Target


HID 
MID
Dis
N
T
Per.
Pval
Gene Names






















778
8547
183
1
3
33.3
0.0493
KIT


778
8547
69 
1
3
33.3
0.0493
SPARC


778
8547
176
2
12
16.7
0.0164
CDH13, 









PDE5A
















TABLE 6







RELATION OF MICRORNAS TO DISEASES BY HOST GENES










HID
MID
H. Gene
Disease(s)













31
7030, 7029
CDH6
167, 157


39
7046, 7045
PAK1
31


42
7052, 7051
MAPK8IP1
64


99
7166, 7165
ITGB3
172, 171, 118, 127, 154, 41, 67, 92, 53, 40,





111, 51, 102


103
7174, 7173
GRM7
162


125
7219, 7218
MOBP
123


127
7223, 7222
PBX1
109


128
7225, 7224
MUC1
110, 133, 31


189
7347, 7346
MYO7A
60


191
7351, 7350
CDH13
31, 176, 133, 110, 51, 167


212
7396, 7395
PAH 162



224 
7420, 7419
TBXA2R
110, 133, 18


232
7438, 7437
NR3C2
57, 98


239
7454, 7453
IL16
112, 56, 92, 160, 18


243
7462, 7461
NRG1
31, 162, 154, 8, 123


246
7468, 7467
ERBB4
31, 51, 154


267
7512, 7511
CCND3
31, 122, 35, 118, 112, 109


291
7568, 7567
ALCAM
118


293
7572, 7571
DAB1
162


301
7588, 7587
PAM 
154, 123, 110


311
7610, 7609
GRIA4
82, 77, 8


338
7664, 7663
SLC1A3
82, 8


355
7698, 7697
NRP2
36


363
7714, 7713
PTPN6
31, 112, 109, 93, 35


364 
7716, 7715
GOLGA5
173


375
7739, 7738
HTR2C
162, 29, 120


390
7769, 7768
COL2A1
135, 60


396
7781, 7780
MLLT2
109


410
7809, 7808
TGFBR3
31


450
7888, 7887
GRIK2
82


466
7920, 7919
TIAM1
157, 70, 31


480
7948, 7947
LAMB1
154, 51


481
7950, 7949
SEMA3F
110


482
7952, 7951
PMS2
118, 79, 51, 154, 151


505
7998, 7997
EPS15
109


506
8000, 7999
ST7
51, 31, 24, 90, 83


560
8108, 8107
CDH13
31, 176, 133, 110, 51, 167


588
8164, 8163
HK2
134, 132, 64


616
8219, 8218
CYLD
166, 157


621
8229, 8228
CHRNA7
144, 8, 24, 162


626
8239, 8238
IL15
167, 110, 31, 92


631
8249, 8248
PTN
118, 31, 167, 154, 141, 133


633
8253, 8252
PAH
162


634 
8255, 8254
ERBB4
31, 51, 154


648
8283, 8282
AMPH
31


654 
8295, 8294
EGFR
51, 31, 167, 133, 110


669
8325, 8324
PTHR1
136


680
8348, 8347
HOXC4
166, 157, 27


681
8350, 8349
MLLT4
109


682
8352, 8351
RANBP17
109


683
8354, 8353
ATP6V1B1
158


689
8366, 8365
NRP2
36


710
8410, 8409
TNC
118, 110, 98, 31, 180, 154, 79, 51


714
8418, 8417
TPO 
60, 174, 102, 61


727
8444, 8443
MLLT2
109


731
8452, 8451
FHIT
133, 110, 42, 31


744
8478, 8477
DSTN
8


780
8551, 8550
S100A1
157


800
8591, 8590
ITGA5
51, 35, 155, 112, 109, 90, 133, 122, 118


803
8597, 8596
MLLT3
109


813
8617, 8616
PTPRG
157, 110, 31


823
8637, 8636
MAP2K5
154


830
8651, 8650
SCN5A
185, 34


838
8667, 8666
GABRA3
82, 29, 47, 123


839
8669, 8668
PTPRN
64, 105, 85


861
8713, 8712
FGFR2
79, 31, 30, 154


897
8785, 8784
TJP2
51, 31, 154


925
8845, 8844
CYP11B2
98


935
8865, 8864
LPP 
110, 109


945
8885, 8884
EPHB2
167


982
8958, 8957
ALK
112, 93


1029
9052, 9051
TACR1
92, 56, 120, 18, 103, 160, 141


1031
9056, 9055
SCN5A
185, 34


1037
9068, 9067
EIF4A1
118, 90


1053
9100, 9099
GRIA4
82, 77, 8


1069
9132, 9131
WNT3A
122


1086
9168, 9167
BCL11A
112, 109, 93


1103
9202, 9201
TP73L
26, 42, 30, 27, 83, 51, 48, 166, 110


1115
9226, 9225
GRIN2B
162, 77, 8


1125
9246, 9245
BIK
31


1132
9260, 9259
GRIA2
8, 77, 82, 162


1138
9272, 9271
GLDC
96


1139
9274, 9273
PRKCD
157, 154


1153
9302, 9301
GPC3
31, 90


1181
9361, 9360
RPS6KB1
31


1241
9481, 9480
ITGA3
31, 154, 118, 79, 51


1253
9505, 9504
ROBO1
31, 157, 110


1259
9517, 9516
MEIS1
109


1264
9527, 9526
RORA
154, 31


1291
9581, 9580
IGF1
60, 133, 31, 51, 67, 110, 92, 105, 64, 132


1297
9593, 9592
CACNA2D2
133


1298
9595, 9594
DAB1
162


1299
9597, 9596
NTRK3
116, 8, 109, 157


1319
9637, 9636
CDH17
109


1345
9689, 9688
CDH23
60


1353
9705, 9704
DLEU2
109


1362
9723, 9722
PTPRG
157, 110, 31


1367
9733, 9732
TPK1
117


1377
9753, 9752
SOAT1
134


1385
9769, 9768
ADCY2
8


1390
9779, 9778
ERCC5
110


1413
9826, 9825
AUTS2
24


1427
9854, 9853
CYP19A1
31, 90, 79, 154


1435
9870, 9869
PTPRF
134, 31


1513
10029, 10028
ABCA4
113


1518
10039, 10038
ITGA3
31, 154, 118, 79, 51


1520
10043, 10042
NGFR
31, 8, 92, 144, 123


1524
10051, 10050
CALCR
160, 136, 31


1541
10084, 10083
ST7 
51, 31, 24, 90, 83


1542
10086, 10085
PTPRF
134, 31


1547
10096, 10095
PTOV1
154


1606
10224, 10223
GPC3
31, 90


1643
10298, 10297
F13A1
48, 56, 49


1662
10338, 10337
CD8B1
92


1663
10340, 10339
HIP1
51, 154, 109


1671
10356, 10355
AUTS2
24


1715
10444, 10443
UBE3A
24


1753
10520, 10519
ADAM12
109, 90, 47, 134, 122, 112


1766
10546, 10545
NSF
162


1771
10556, 10555
LPP
110, 109


1776
10566, 10565
SDC2
24


1801
10619, 10618
IGF1R
110, 154, 118, 31


1812
10641, 10640
IL15
167, 110, 31, 92


1866
10749, 10748
HMGA2
79, 110


1877
10771, 10770
GRIK2
82


1879
10775, 10774
RORA
154, 31


1890
10799, 10798, 10797, 10796
EIF4A2
88, 112


1900
10819, 10818
SREBF2
134, 95, 51, 154


1911
10841, 10840
ELAVL4
167


1915
10849, 10848
MTAP
110, 109, 133


1932
10884, 10883
HOXC5
112, 42


1950
10920, 10919
WWOX
122, 83, 31


1958
10936, 10935
CALCR
160, 136, 31


1973
10968, 10967
TGIF
83


2008
11038, 11037
GYPC
114


2009
11040, 11039
GYPC
114


2028
11078, 11077
CSEN
8


2037
11096, 11095
FYN
112, 109, 92, 157


2125
11275, 11274
NISCH
98


2142
11309, 11308
TMEFF2
154, 51, 30


2146
11317, 11316
HLA-DRB5
109, 105, 64, 123


2149
11325, 11324
GNAO1
8


2156
11340, 11339
FLT4
110, 31, 90, 109, 112, 154, 133, 51


2182
11403, 11402
HTR2C
162, 29, 120


2210
11461, 11460
IMP-1
51, 31


2232
11507, 11506
TPK1
117


2265
11573, 11572
CSEN
8


2268
11579, 11578
CASP8
8, 167, 157, 92, 51, 31, 133, 110


2269
11581, 11580
COL4A2
157, 154


2281
11605, 11604
VWF
64, 53, 31, 105, 103, 92, 132


2283
11609, 11608
KCNH1
42, 31


2285
11613, 11612
BIK
31


2287
11617, 11616
PTPRG
157, 110, 31


2340
11723, 11722
CRKL
109


2379
11804, 11803
CTNNBIP1
51, 118


2399
11844, 11843
RANBP17
109


2412
11870, 11869
ERBB4
31, 51, 154


2417
11886, 11885
GPC1
31


2431
11914, 11913
ROBO1
31, 157, 110


2451
11954, 11953
SCN5A
185, 34


2473
11998, 11997
ABAT
162


2480
12012, 12011
CEACAM5
31, 110, 133, 51


2482
12016, 12015
TP73
118, 112, 110, 51, 35, 31, 109, 90, 59


2494
12043, 12042
PBX1
109


2498
12051, 12050
MECP2
24, 133


2517
12089, 12088
PRKCG
31, 8, 154, 51


2538
12131, 12130
TUB 
134


2543
12141, 12140
ST7
51, 31, 24, 90, 83


2549
12153, 12152
HLF
109


2551
12157, 12156
SEMA3F
110


2558
12171, 12170
APLP2
8


2583
12221, 12220
RANBP17
109


2589
12236, 12235
NTRK3
116, 8, 109, 157


2595
12248, 12247
C3
51, 31, 8, 105, 92, 64, 134, 110


2615
12288, 12287
GRIK1
82, 77, 70, 10


2636
12329, 12328
PBX1
109


2651
12359, 12358
DLEU2
109


2662
12381, 12380
DAPK1
51, 31, 30, 112, 110, 109, 176, 133


2668
12393, 12392
CDC27
118


2677
12411, 12410
PAH
162


2734
12528, 12527
ALK
112, 93


2769
12597, 12596
ED1
166, 118


2781
12621, 12620
GRM7
162


2788
12635, 12634
HDGF
90, 83


2808
12677, 12676
DPYD
30, 157, 106, 83, 51, 31


2831
12727, 12726
CAST
98, 63, 8, 160, 111, 109


2841
12747, 12746
TBX2
31


2853
12771, 12770
CALCR
160, 136, 31


2860
12785, 12784
MYH7
129, 100


2861
12787, 12786
AUTS2
24


2881
12830, 12829
SERPINA5
172


2883
12834, 12833
CACNA1G
109, 51


2887
12842, 12841
CDH13
31, 176, 133, 110, 51, 167


2892
12852, 12851
ITGA5
51, 35, 155, 112, 109, 90, 133, 122, 118


2917
12902, 12901
MITF
118, 60


2918
12904, 12903
DYSF
129


2932
12932, 12931
MME 
167, 133, 110, 8


2938
12944, 12943
RORA
154, 31


2943
12954, 12953
ST7 
51, 31, 24, 90, 83


2966
13000, 12999
PTPRF
134, 31


2973
13014, 13013
KCNQ1
60, 21


2980
13028, 13027
MEIS1
109


2998
13064, 13063
HOXB3
109


3003
13074, 13073
CSEN
8


3023
13119, 13118
PPP2R1B
51, 31, 110


3039
13154, 13153
DYSF
129


3052
13180, 13179
CDH23
60


3056
13191, 13190
ELN
110


3105
13293, 13292
AUTS2
24


3172
13430, 13429
AUTS2
24


3178
13442, 13441
OTOF
60


3214
13514, 13513
FUT8
138, 51


3222
13530, 13529
HLF
109


3227
13540, 13539
TCF4
162, 29


3250
13586, 13585
ACTN4
31


3300
13686, 13685
ACPP
181, 154, 30


3308
13702, 13701
AR
154, 92, 110, 51, 8, 31


3312
13710, 13709
GLP1R
132, 64


3338
13762, 13761
KCNQ1
60, 21


3361
13811, 13810
RORA
154, 31


3409
13907, 13906
GRIA3
82, 77, 29


3422
13933, 13932
DDC 
167, 105, 162, 29, 24, 144, 36, 64, 23, 133


3427
13943, 13942
PTPRG
157, 110, 31


3489
14066, 14065
EDNRA
64, 51, 42, 132, 108, 98, 31, 174, 134


3504
14096, 14095
COPEB
154


3542
14173, 14172
MLLT2
109


3561
14211, 14210
GYPC
114


3592
14272, 14271
FKBP5
154 


3608
14304, 14303
BCL11A
112, 109, 93


3613
14318, 14317, 14316
HTR2C
162, 29, 120


3618
14328, 14327
ALCAM
118


3684
14460, 14459
ERBB4
31, 51, 154


3693
14478, 14477
ZNFN1A1
112, 109


3754
14601, 14600
EPB41
114


3756
14605, 14604
SLC7A5
51


3778
14651, 14650
SDC2
24


3794
14683, 14682
ST7
51, 31, 24, 90, 83


3803
14702, 14701
WT1
31, 133, 110


3856
14808, 14807
STS
31


3878
14855
ADAM12
109, 90, 47, 134, 122, 112


3885
14869, 14868
FGFR2
79, 31, 30, 154


3890
14879, 14878
C3
51, 31, 8, 105, 92, 64, 134, 110


3902
14903, 14902
DLEU2
109


3924
14946, 14945
HOXC8
42, 51


3928
14954, 14953
PTPRN2
64, 105


3929
14956, 14955
HTR2C
162, 29, 120


3935
14968, 14967
GNAO1
8


3955
15008, 15007
PRDX1
70, 8, 109


3997
15099, 15098
PRKCA
51, 31, 150, 110, 64, 8, 132


4000
15106, 15105
CDH5
118


4006
15118, 15117
RUNX1
109, 160


4014
15134, 15133
GNAO1
8


4020
15146, 15145
AMPH
31


4025
15156, 15155
ETS1
110, 51, 31


4059
15222, 15221
APPBP2
31


4069
15242, 15241
MLLT2
109


4085
15274, 15273
ALK
112, 93


4086
15276, 15275
PTN
118, 31, 167, 154, 141, 133


4136
15376, 15375
PTPRN2
64, 105


4145
15394, 15393
APBB1
144, 8


4152
15408, 15407
DYSF
129


4160
15424, 15423
PLCB1
167


4162
15428, 15427
DPYD
30, 157, 106, 83, 51, 31


4171
15452, 15451
MLLT3
109


4179
15468, 15467
ALK
112, 93


4211
15532, 15531
TRPM1
118


4217
15544, 15543
IGFBP2
64, 31, 51, 132, 110, 105, 134


4229
15568, 15567
ALK
112, 93


4232
15574, 15573
LPP
110, 109


4270
15653, 15652
NF1
31, 118, 110, 51, 167


4275
15663, 15662
MGAT5
88, 51, 118, 90


4286
15685, 15684
MST1R
133, 31, 110, 51


4289
15691, 15690
NTRK1
31, 116, 173, 167, 8


4300
15713, 15712
FHIT
133, 110, 42, 31


4315
15743, 15742
APBA2
75, 51, 8


4323
15759, 15758
CACNA1A
120, 61


4344
15801, 15800
GRIA3
82, 77, 29 


4352
15817, 15816
COL11A2
60


4360
15833, 15832
RAD51L1
110


4384
15885, 15884
TERT
110, 51, 31, 133


4389
15895, 15894
APBA2
75, 51, 8


4391
15899, 15898
TPO
60, 174, 102, 61


4401
15919, 15918
TMC1
60


4402
15921, 15920
AK1
86


4406
15929, 15928
MLLT3
109


4410
15936
CDK6
133, 51, 31, 167


4422
15960, 15959
VWF
64, 53, 31, 105, 103, 92, 132


4423
15962, 15961
NR3C2
57, 98


4446
16008, 16007
FHIT
133, 110, 42, 31


4454
16024, 16023
DCC
51


4469
16054, 16053
GRIA2
8, 77, 82, 162


4470
16056, 16055
ATP1A1
98, 64, 8, 105


4472
16060, 16059
PTPRG
157, 110, 31


4476
16068, 16067
SCG3
154


4477
16070, 16069
CBFA2T1
109


4480
16076, 16075
FKBP5
154


4498
16115
ERBB4
31, 51, 154


4509
16137, 16136
HOXB3
109


4529
16177, 16176
GRM7
162


4547
16213, 16212
CDX1
106, 51


4587
16293, 16292
SLC7A5
51


4589
16297, 16296
RANBP17
109


4596
16311, 16310
CACNA1A
120, 61


4608
16335, 16334
APBA2
75, 51, 8


4618
16355, 16354
NTRK2
10, 154, 8, 162


4619
16357, 16356
OTOF
60


4628
16375, 16374
PTPRN2
64, 105


4659
16437, 16436
CACNA1A
120, 61


4660
16439, 16438
CUBN
117


4672
16464, 16463
MTAP
110, 109, 133


4674
16468, 16467
DYSF
129


4680
16480, 16479
PTPRN
64, 105, 85


4695
16510, 16509
PRKCA
51, 31, 150, 110, 64, 8, 132


4706
16533, 16532
KCNH1
42, 31


4711
16543, 16542
GRIA3
82, 77, 29


4714
16549, 16548
GLP1R
132, 64


4723
16567, 16566
THRA
157, 150


4761
16643, 16642
PSG1
70


4792
16706, 16705
SEMA3F
110


4802
16729, 16728
MPZ
112


4858
16840, 16839
AUTS2
24


4864
16852, 16851
NF1
31, 118, 110, 51, 167


4866
16856, 16855
RPA1
110, 51, 31, 133


4872
16868, 16867
PTPRN
64, 105, 85


4886
16896, 16895
CD3Z
93, 157, 111


4897
16918, 16917
MSN 
70, 92, 160


4898
16920, 16919
GAP43
8, 62, 10, 162, 29


4900
16924, 16923
PAX2
157


4909
16942, 16941
MYH6
129, 100


4919
16962, 16961
HK2
134, 132, 64


4929
16982, 16981
ZNFN1A1
112, 109


4936
16996, 16995
TNC
118, 110, 98, 31, 180, 154, 79, 51


4941
17006, 17005
PLCB1
167


4959
17043, 17042
PTPRF
134, 31


5001
17130, 17129
ERBB2
110, 133, 154, 26, 176, 167, 51, 31, 30


5026
17183, 17182
YWHAG
118


5037
17205, 17204
KCNN3
162, 29


5040
17211, 17210
DPYD
30, 157, 106, 83, 51, 31


5070
17272, 17271
MUC1
110, 133, 31


5079
17290, 17289
CDC10
112


5126
17384, 17383
GRB7
83, 31


5134
17400, 17399
HTR2C
162, 29, 120


5139
17410, 17409
ROBO1
31, 157, 110


5143
17418, 17417
GRIA2
8, 77, 82, 162


5166
17464, 17463
ALK 
112, 93


5174
17480, 17479
CENPF
90, 31


5189
17510, 17509
PROS1
172


5231
17594, 17593
CTNND2
154


5263
17659, 17658
BCL9
112, 109


5309
17751, 17750
MLLT3
109


5331
17796, 17795
PTPRF
134, 31


5332
17798, 17797
GRIA4
82, 77, 8


5350
17834, 17833
PAPPA
53, 70


5363
17860, 17859
GRIN2B
162, 77, 8


5406
17948, 17947
SYN2
8, 162


5409
17954, 17953
DYSF
129


5504
18146, 18145
ST7
51, 31, 24, 90, 83


5518
18174, 18173
CPB2
172, 127


5556
18250, 18249
MAP2K5
154


5563
18264, 18263
PRKCA
51, 31, 150, 110, 64, 8, 132


5603
18344, 18343
MUC1
110, 133, 31


5630
18397, 18396
FMR2
84


5636
18409, 18408
PRDM2
90, 51, 79, 31, 112, 110


5638
18413, 18412
THRB
157, 154, 150, 133, 31, 167


5647
18433, 18432
MOBP
123


5670
18479, 18478
APBA2
75, 51, 8


5686
18511, 18510
LPA
52, 8


5697
18535, 18534
ACTN4
31


5711
18567, 18566
CDH13
31, 176, 133, 110, 51, 167


5721
18587, 18586
SREBF1
132, 92, 64, 134


5725
18595, 18594
SCN5A
185, 34


5738
18621, 18620
TCF4
162, 29


5745
18635, 18634
HTR2C
162, 29, 120


5765
18675, 18674
CSEN
8


5803
18754, 18753
PTPRF
134, 31


5820
18789, 18788
FMR2
84


5827
18803, 18802
HOXA3
109


5832
18813, 18812
HSD11B1
134


5833
18815, 18814
GRIN2B
162, 77, 8


5869
18887, 18886
HSPG2
133, 110, 31, 8


5890
18931, 18930
DAB1
162


5901
18955, 18954
TIAM1
157, 70, 31


5913
18978, 18977
ITGA11
133


5923
18998, 18997
PTCH
30, 27, 166, 83, 31


5942
19036, 19035
DCC
51


5943
19038, 19037
SFTPB
110


5967
19091, 19090
GFRA1
116


6006
19170, 19169
CDH13
31, 176, 133, 110, 51, 167


6025
19207, 19206
AUTS2
24


6044
19245, 19244
BCL11B
109


6057
19271, 19270
PTPRG
157, 110, 31


6070
19297, 19296
CXADR
154, 30


6082
19321, 19320
GABRA3
82, 29, 47, 123


6118
19393, 19392
DMD
129


6127
19411, 19410
PRKCG
31, 8, 154, 51


6151
19459, 19458
STS
31


6152
19461, 19460
HTR2C
162, 29, 120


6159
19475, 19474
PARK2
144, 61


6164
19485, 19484
ED1
166, 118


6213
19583, 19582
NCOR2
109, 31


6220
19597, 19596
CRHR1
57


6233
19624, 19623
GRM3
162, 29


6255
19668, 19667
LIPC
97, 64, 53, 132, 105


6272
19702, 19701
TIE
109, 31, 4, 166, 157, 118


6285
19728, 19727
PAX5
112


6289
19736, 19735
MME 
167, 133, 110, 8


6327
19812, 19811
IGSF4
133, 110, 90, 154, 31


6329
19816, 19815
GRM7
162


6338
19834, 19833
RAD51L1
110


6342
19842, 19841
GOLGA5
173


6344
19846, 19845
BAI1
133, 110, 51


6385
19929, 19928
CTNNA1
152, 51


6398
19956, 19955
AUTS2
24


6408
19976, 19975
LGI1
82


6418
19996, 19995
KCNQ3
82


6420
20000, 19999
MYO7A
60


6421
20002, 20001
NTRK3
116, 8, 109, 157


6447
20060, 20059
CHD4
63


6503
20172, 20171
ACVR1B
150, 140


6505
20176, 20175
CDK6
133, 51, 31, 167


6521
20208, 20207
SGCD
100, 129


6542
20252, 20251
HMGA2
79, 110


6571
20311, 20310
HK2 
134, 132, 64


6575
20319, 20318
DBP 
87


6577
20323, 20322
MTAP
110, 109, 133


6580
20329, 20328
TGFBI
83


6582
20333, 20332
KCNQ3
82


6588
20345, 20344
SLC7A5
51


6600
20369, 20368
PTPRF
134, 31


6602
20373, 20372
FLJ22795
51, 110


6611
20391, 20390
TGM1
133, 8


6612
20393, 20392
CHRNB1
124


6614
20397, 20396
PAX2
157


6670
20516, 20515
GPC3
31, 90


6671
20518, 20517
SCN5A
185, 34


6676
20528, 20527
CACNA1G
109, 51


6696
20571, 20570
PRKCA
51, 31, 150, 110, 64, 8, 132


6742
20665, 20664
GRIK4
162, 82


6756
20693, 20692
HTR2C
162, 29, 120


6760
20701, 20700
NEB 
129


6776
20736, 20735
TGFBR3
31


6779
20742, 20741
HTR2C
162, 29, 120


6789
20762, 20761
GRIA3
82, 77, 29


6811
20806, 20805
CPB1
141


6819
20822, 20821
HD
8, 51


6821
20826, 20825
BCL11B
109


6835
20854, 20853
NLGN3
24


6844
20872, 20871
MEST
110, 51, 31


6846
20876, 20875
CA12
31, 157


6847
20878, 20877
GABRA3
82, 29, 47, 123


6867
20918, 20917
BIK
31


6887
20961, 20960
CDH13
31, 176, 133, 110, 51, 167


6918
21023, 21022
PAX3
118, 60


6960
21107, 21106
PRKDC
51, 109
















TABLE 7







TISSUE AND DISEASE CODES FOR TABLE 2 AND 3








Tissue or Disease name
ID











Prostate adenocarcinoma
1


Lung adenocarcinoma
2


Skeletal muscle
3 


Spleen
4


Lung
5


Lung adenocarcinoma
6


Placenta
7


Embryonic Stem cells
8


Prostate adenocarcinoma
9


Prostate
10


Brain Substantia Nigra
11


Testis
12


Uterus carcinoma cell line (HeLa)
13


Adipose
14


Lung carcinoma cell line (H1299)
15


Lung carcinoma cell line (H1299) with P53
16


Overy and Small Intestine (mixture)
17


Embryonic Stem carcinoma cells
18


Brain
19


Brain with Alzheimer
20


Uterus carcinoma cell line (cMagi) with HIV
21


T cell line (MT2)
22


T cell line (MT2) with HIV
23


Placenta and Brain Substantia Nigra (mixture)
24


B cell line
25


T cell line (MT2) with HIV and Brain Substantia Nigra
26


(mixture)



T cell line (MT2) with HIV and Lung adenocarcinoma
27


(mixture)
















TABLE 8







DISEASE CODES FOR TABLES 5 AND 6








Disease Name
ID











Addisons disease
1


Adenovirus
2


Adrenal cortical carcinoma
3


Aids
4


Allergic contact dermatitis
5


Alopecia
6


Alpha thalassemia
7


Alzheimer
8


Amyloidosis
9


Amyotrophic Lateral Sclerosis
10


Anal cancer
11


Anorexia Nervosa
12


Antisocial Personality Disorder
13


Aortic Aneurysm
14


Aortic stenosis
15


Aplastic anemia
16


Appendiciti
17


Asthma
18


Atherosclerosis
19


Atopic dermatiti
20


Atrial fibrillation
21


Atrophic gastriris
22


Attention Deficit Disorder 
23


Autism
24


Bacillary Dysentery
25


Barrett Esophagus
26


Basal cell carcinoma
27


Beta Thalassemia
28


Bipolar Disorder
29


Bladder cancer
30


Breast cancer
31


Bronchiectasis
32


Bulimia
33


Bundle-Branch Block
34


Burkitt lymphoma
35


Carcinoid
36


Cataract
37


Celiac Disease
38


Cerebral Hemorrhage
39


Cerebral Infarction
40


Cerebrovascular Accident
41


Cervical cancer
42


Chlamydia
43


Cholelithiasis
44


Cholestasis
45


Chronic obstructive pulmonary disease
46


Cirrhosis
47


Cleft Lip
48


Cleft Palate
49


Clostridium
50


Colorectal cancer
51


Coronary artery disease
52


Coronary disease
53


Coronary spasm
54


Coxsackievirus
55


Crohn disease
56


Cushing Syndrome
57


Cystic fibrosis
58


Cytomegalovirus
59


Deafness
60


Dementia
61


Depressive Disorder
62


Dermatomyositis
63


Diabetes Mellitus
64


Diabetic Nephropathy
65


Diabetic Neuropathies
66


Diabetic Retinopathy
67


Diphtheria
68


Diverticulitis
69


Down Syndrome
70


Duodenal Neoplasms
71


Duodenal Ulcer
72


Dyslexia
73


E.coli
74


EBV
75


Emphysema
76


Encephalitis
77


Endocarditis
78


Endometrial carcinoma
79


Enterovirus
80


Enuresis
81


Epilepsy
82


Esophageal cancer
83


Fragile X Syndrome
84


Gestational Diabetes
85


Hemolytic anemia
86


Hemophilia
87


Hepatitis
88


Hepatocellular carcinoma
89


Hepatocellular carcinoma
90


Herpes
91


HIV
92


Hodgkin Disease
93


HTLV
94


Hypercholesterolemia
95


Hyperglycemia
96


Hyperlipidemia
97


Hypertension
98


Hypertrophic Cardiomopathy
99


Hypertrophic cardiomyopathy
100


Infectious Mononucleosis
101


Infertility
102


Inflammatory Bowel Diseases
103


Influenza
104


Insulin-Dependent Diabetes Mellitus
105


Intestinal Neoplasms
106


Kidney Failure
107


Left Ventricular Dysfunction
108


Leukemia
109


Lung cancer
110


Lupus Erythematosus
111


Lymphoma
112


Macular Degeneration
113


Malaria
114


Measles
115


Medullary thyroid carcinoma
116


Megaloblastic anemia
117


Melanoma
118


Meningitis
119


Migraine
120


Multiinfarct dementia
121


Multiple Myeloma
122


Multiple Sclerosis
123


Myasthenia Gravis
124


Mycobacterium
125


Mycoplasma
126


Myocardial Infarction
127


Myocarditis
128


Myopathy
129


Nephrogenic diabetes insipidus
130


Nephrolithiasis
131


Non-Insulin-Dependent Diabetes Mellitus 
132


Nonsmall cell lung cancer
133


Obesity
134


Osteoarthritis
135


Osteoporosis
136


Otitis Media
137


Ovarian cancer
138


Pagets Disease
139


Pancreatic cancer
140


Pancreatitis
141


Papilloma
142


Paramyxoviridae
143


Parkinson
144


Peptic Ulcer
145


Peripheral Vascular Diseases
146


Peritonitis
147


Pertussis
148


Picornaviridae
149


Pituitary tumor
150


Polyposis
151


Polyposis coli
152


Postpartum depression
153


Prostate cancer
154


Psoriasis
155


Psoriatic arthritis
156


Renal cell carcinoma
157


Renal Tubular Acidosis
158


Respiratory Syncytial Virus
159


Rheumatoid arthritis
160


Rhinitis
161


Schizophrenia
162


Sickle cell anemia
163


Sideroblastic anemia
164


Sinusitis
165


Skin Neoplasms
166


Small cell carcinoma
167


Stroke
168


Sudden cardiac death
169


Syphilis
170


Thrombocytopenia
171


Thrombosis
172


Thyroid carcinoma
173


Thyroiditis
174


Toxoplasmosis
175


Transitional cell carcinoma
176


Trichomonas vaginitis
177


Tuberculosis 
178


Turner Syndrome
179


Ulcerative colitis
180


Urethral neoplasms
181


Urinary calculi
182


Urticaria
183


Vascular dementia
184


Ventricular Fibrillation
185


Ventricular tachycardia
186


Virus Diseases
187
















TABLE 9







RELATION OF TARGET GENES TO DISEASE








Gene Name
Disease Code





A2M
8, 76, 144


AAAS 1



AANAT
27, 118


AARS
63


AAT1
14


AAT2
14


ABAT
162


ABCA1
53


ABCA4
113


ABCB1
31, 51, 92, 167, 110, 133, 152


ABCB11
45


ABCB4
31, 44, 45


ABCB7
164


ABCC1
31, 110


ABCC2
51, 90


ABCC3
30, 110, 133, 167


ABCC4
110


ABCC5
92, 110


ABCC6
109


ABCC8
64, 132


ABCD1
1


ABCD3
51


ABCG2
31, 109, 110


ABL1
31, 51, 109


ABL2
109


ABO
30, 109


ABP1
42, 79, 154


ACE
8, 31, 65, 110, 127, 133


ACHE
8, 10


ACO1
8


ACP1
64, 105, 134


ACP5
31, 107, 160


ACPP
30, 154, 181


ACR
102


ACTA1
129


ACTB
8, 31, 51, 167


ACTC
100, 129, 162


ACTG1
60


ACTN4
31


ACVR1
31, 150


ACVR1B
140, 150


ACVR2
150


ACY1
110, 157, 167


AD2
8


AD5
8


AD6
8


AD7C-NTP
8


AD8
8


ADA
86


ADAM10
21, 135


ADAM11
31


ADAM12
47, 90, 109, 112, 122, 134


ADAM17
160


ADAM2
8


ADAMTS13
4, 171


ADAMTS4
160


ADCY1
8


ADCY2
8


ADCY8
8


ADCYAP1
110, 140, 150, 154, 167


ADD1
98


ADFN 
60


ADH1B
83


ADH1C
31, 127


ADM
3, 52, 64, 132, 154, 79, 85, 108


ADORA1
8, 58, 186


ADORA3
118


ADPRT
31, 51, 110


ADRA2A
8, 23, 62, 134, 162


ADRA2C
23


ADRB1
8, 52, 53, 98, 134


ADRB2
8, 18, 58, 132, 134, 64, 97, 98


ADRB3
53, 64, 67, 134, 97, 98, 132


ADRBK1
53, 58, 98, 160


ADSL 
24


AF15Q14
109


AF3P21
109


AF5Q31
109


AFM
90


AFP
31, 154


AGER
8, 9, 64, 146, 105, 132, 133


AGR2
31


AGRN
8


AGRP
12, 134


AGT
8, 64, 65, 98, 105, 132


AGTR1
3, 15, 53, 127, 98, 99, 105, 64, 65, 95


AGTR2
57, 95, 108


AHR
31, 79, 110, 154


AIF1
40


AIRE 
1, 64, 105, 174


AK1
86


AKAP12
110, 124


AKR1B1
64, 66, 90, 105


AKR1B10
90


AKT1
10, 31, 64, 133, 154, 162, 79, 110, 132


AKT2
31, 83, 110


AKT3
31, 51, 110, 154


ALAS2
164


ALB
4, 8, 31, 133, 167, 105, 110, 132, 51, 64, 92


ALCAM
118


ALDH1A1
133, 157


ALDH3A1
31, 83, 90


ALDOA
110


ALK
93, 112


ALMS1
134


ALOX12
64, 98, 132, 154


ALOX15
51, 154


ALOX15B
154


ALOX5
18, 31, 92, 140, 154, 180, 109, 110, 112


ALOX5AP
18, 92, 127, 168


ALPL
31


ALPP
70, 79


ALS2
10


ALS4
10


ALS6
10


ALSFTD
10, 61


AMACR
51, 154


AMBP
92, 110


AMFR
30, 118, 133, 154


AMN 
117


AMPH 
31


AMT
96


AMY2A
64, 105


ANG
31, 42, 51, 109, 118, 154


ANGPT1
31, 42, 133


ANGPT2
31, 51, 90


ANGPT4
31, 157


ANON 
12 


ANP32A
92


ANPEP
51, 123


ANXA1
31, 83, 110, 154


ANXA2
110, 154, 167


ANXA3
43


AOC3
8, 61, 103, 107, 121


AOCH
49


AOMS1
134


AOMS2
134


APBA1
51


APBA2
8, 51, 75


APBB1
8, 144


APC
31, 51, 83, 167, 151, 152, 154, 106, 110, 133


APCS
8, 9, 64, 132


APEH
157


APEX1
10, 42, 51, 109


APLP1
8


APLP2
8


APM1
12, 64, 92, 98, 132, 134


APOA2
64, 95, 98, 127, 132


APOA4
8, 9, 53, 134, 141, 105, 127, 132, 64, 95, 97


APOB
4, 8, 31, 105, 132, 64, 92, 95


APOBEC1
51


APOBEC3G
92


APOC1
8, 64, 95, 97, 132


APOC2
8, 64, 132


APOC3
8, 53, 64, 134, 97, 105, 132


APOD 
8, 29, 31, 132, 162, 64, 123, 127


APOH 
64, 111


APOL1
162


APOL2
162


APOL4
162


APP
8, 9, 31, 123, 162


APPBP2
31


APRIN
154


APRT
131, 182


APXL
118


AQP1
157


AQP2
81, 130


AR
8, 31, 51, 92, 110, 154


AREG
30, 31, 42, 155, 133, 51, 154


ARG2
64


ARH
95


ARHA
31, 51, 89, 154, 159, 90, 110, 118


ARHB
31


ARHC
31


ARHI
31, 138


ARHU
31, 51, 157


ARMD1
113


ARMET
140


ARNT
31, 109


ARVCF
29


ARX
82


AS1
18


ASAH1
20, 106, 154


ASC
17, 31


ASCL1
167


ASGR1
47, 88, 90


ASPSCR1
157


ATF1
118


ATF2
31, 110, 118


ATF3
51


ATF6
8


ATIC
112


ATM
31, 93, 112


ATP10A
24


ATP1A1
8, 64, 98, 105


ATP1A2
120


ATP1A4
120


ATP2A1
129


ATP2A2
29


ATP6B1
60, 158


ATP6V0A4
158


ATP6V1B1
158


ATP6V1G2
160


ATP7B
31


ATP8B1
45


ATPIF1
129


ATRX
31, 51, 112


AURKB
51


AUTS1
24


AUTS2
24


AUTS3
24


AUTS4
24


AVP
110, 167


AVPR1A
24, 57, 98


AVPR1B
36, 57, 110, 150


AVPR2
130


AXIN1
90


AXIN2
51


AXL
51, 90, 109, 110, 167


AZGP1
31, 154


AZU1
8


B2M
4, 8, 9, 123, 133, 92, 110, 118, 31, 51, 77


B3GALT1
51


B3GALT2
154


BAALC
109


BACE
8


BACE2
8, 31, 51, 70


BAD
8, 109, 110, 118


BAG1
31, 42, 109


BAI1
51, 110, 133


BAK1
8, 31, 51, 166, 110, 133, 154


BAL
112


BARD1
31


BAX
8, 31, 51, 123, 167, 110, 133


BBP
8


BCAR1
2, 31, 118


BCAR3
31


BCAS1
31, 51


BCAS2
31


BCHE
8, 110


BCL1
112


BCL10
31, 42, 51, 157, 112, 122, 154, 79, 109, 110


BCL11A
93, 109, 112


BCL11B
109


BCL2
4, 8, 31, 167, 112, 123, 133, 51, 92, 110


BCL2L1
8, 31, 51, 167, 123, 133, 154, 92, 110, 122


BCL3
48, 49, 83, 109, 112


BCL6
4, 31, 112


BCL7A
93, 112


BCL8
112


BCL9
109, 112


BCMP11
31


BCPR
31


BDKRB1
160


BDKRB2
18, 64, 92, 132, 154, 160


BDNF
8, 123


BF
174


BFSP2
37


BGLAP
31, 64, 92, 136, 105, 110, 132


BID
90, 154


BIK
31


BIN1
31, 118, 154


BIRC2
42, 83, 123


BIRC3
110, 112, 122, 123


BIRC4
51, 109, 122, 133


BIRC5
31, 51, 110, 133, 140


BIRC7
118


BLCAP
30, 157


BLM
51, 106, 109


BLMH
8, 35, 112


BLR1
4, 92, 109, 112, 122, 123


BLZF1
109


BMP1
154


BMP2
154


BMP3
154


BMP6
154


BMPR1A
151


BMPR2
98, 154


BMX
154


BPGM 
86


BRAF
51, 110, 118


BRCA1
31, 51, 138


BRCA2
31, 51, 110, 133, 140, 154


BRCA3
31


BRCATA
31


BRCD1
31


BRIP1
31


BRS3
110, 134


BSG
92, 118, 166


BSND
60


BST2
122


BTC
79


BUB1
51, 109, 110, 112, 133


BUB1B
51, 109, 112


BULN
33


BZRP
8, 31, 162


C11orf17
31, 154


C13orf1
109


C1QA
111


C1QB
8, 10


C1R
8, 77, 123


C1S
8, 111


C21orf107
70


C21orf33
60


C3
8, 31, 51, 110, 134, 64, 92, 105


C3AR1
18, 119, 123


C4A
64, 105, 111, 127


C4BPA
148


C4BPB
148


C5
8, 92, 119, 127


C5orf7
109


C5R1
18, 92, 119, 123


C6orf15
155


C6orf18
155


C7
8


C9
8, 63, 119, 123, 127


CA1
109, 133, 141


CA12
31, 157


CA2
158


CA9
31, 42, 51, 118, 133, 157


CAAR 
37


CAB2
31


CACNA1A
61, 120


CACNA1G
51, 109


CACNA2D2
133


CACNB2
82, 167


CACNB4
82


CALB1
8, 10, 51, 82, 144


CALB2
8, 51, 162


CALCA
110, 136, 167


CALCB
116, 160


CALCR
31, 136, 160


CALCRL
98


CALR
35, 38, 51, 160, 111, 112, 154


CANX
31, 58


CAPN10
64, 132


CARD15
56, 103, 156, 180


CARD4
103


CART
134


CASP1
4, 31, 51, 92, 123


CASP10
93, 112, 133


CASP2
8, 109


CASP3
8, 31, 42, 154, 110, 123, 133, 51, 92, 109


CASP5
51, 79, 133


CASP6
31, 118, 154


CASP7
31, 51, 154, 157


CASP8
8, 31, 51, 157, 167, 92, 110, 133


CASP9
4, 8, 31, 122, 133, 51, 90, 110


CASQ2
186


CASR
31, 64, 132, 136


CAST
8, 63, 98, 109, 111, 160


CAT
4, 8, 31, 110, 132, 133, 51, 64, 92


CATM
37


CAV1
31, 47, 51, 154, 155, 83, 92, 110


CAV2
83, 154


CBFA2T1
109


CBFA2T3
31, 109


CBL
109, 112


CBS
19, 70


CCA1
37


CCAL1
135


CCFDN
37


CCK
8, 64, 132, 167


CCKAR
44, 64, 132, 134, 141, 162


CCKBR
51, 64, 110, 132, 162, 167


CCL1
5, 92, 125, 159


CCL11
18, 20, 56, 165, 180, 183, 92, 93, 159


CCL13
18, 155


CCL17
5, 18, 20, 93, 109


CCL2
8, 31, 64, 167, 123, 132, 133, 92, 105, 110


CCL20
155, 160


CCL21
20


CCL24
18


CCL3
4, 31, 51, 92, 94, 123


CCL4
4, 8, 31, 123, 133, 92, 94, 110


CCL5
31, 42, 92, 94, 123, 133


CCL7
18, 20, 92, 123, 180


CCL8
92, 112


CCNA1
109


CCNB1
8, 31, 51, 110, 133


CCNC
31, 109


CCND1
31, 51, 110, 180, 133, 112, 122, 167


CCND2
31, 51


CCND3
31, 35, 109, 112, 118, 122


CCNE1
31, 110, 133, 167


CCNE2
31, 42, 109, 133, 167


CCNI
31


CCNP
37


CCNT1
92


CCR1
88, 91, 92, 123, 160


CCR2
4, 18, 61, 135, 136, 160, 92, 122, 123


CCR3
18, 20, 92, 93, 123


CCR4
18, 20, 88, 112, 123, 92, 93, 111


CCR5
4, 61, 92, 123


CCR6
94, 109, 112, 122, 160


CCR7
31, 59, 92, 118, 93, 109, 112


CCR8
18, 46, 92, 123


CCS
10


CCSSO
37


CCT
37


CCV
37


CD14
4, 31, 51, 92, 123


CD151
110, 133


CD163
109, 123, 160


CD19
31, 51, 92, 110


CD1A
31, 92


CD1B
20, 123


CD1C
111


CD1D
64, 105, 109


CD22
92


CD24
31, 35, 90, 133, 154, 167, 109, 110, 112


CD33
31


CD34
31, 92


CD36
31, 64, 92, 167, 114, 171, 110, 132


CD37
109, 112


CD38
4, 64, 92, 105, 132


CD3G
92


CD3Z
93, 111, 157


CD4
4, 31, 92, 111


CD44
31, 51, 92, 133, 157, 109, 110, 123 


CD47
109


CD58
31, 51, 64, 92, 105


CD59
4, 8, 31, 114, 51, 92, 110


CD63
92, 118


CD68
4, 92


CD69
18, 31, 64, 160, 178, 92, 105, 111


CD74
110, 133, 167


CD80
31, 51, 64, 123, 105, 92, 110


CD83
31, 92, 109, 157


CD86
31, 51, 64, 92, 105, 123


CD8A
38, 88, 92, 93, 109, 157


CD8B1
92


CD9
31, 51, 133, 167


CD97
112, 160


CDA
109


CDC10
112


CDC2
8, 31, 51, 167, 92, 110, 133


CDC25A
31, 51, 83, 112, 133


CDC25B
31, 51, 83, 112, 133


CDC25C
79, 112, 166


CDC27
118


CDC2L1
112, 118


CDC2L2
118


CDC42
31, 51


CDH1
31


CDH11
31, 51, 154


CDH13
31, 51, 110, 133, 167, 176


CDH17
109


CDH23
60


CDH5
118


CDH6
157, 167


CDK10
31, 112


CDK2
31, 42, 51, 110, 133


CDK4
8, 31, 51, 110, 118, 133


CDK5
8, 10


CDK5R1
8, 70


CDK6
31, 51, 133, 167


CDK7
31, 51


CDK9
92


CDKN1A
31, 51, 79, 133, 167, 180, 90, 92, 110


CDKN1B
31, 110, 133, 167


CDKN1C
3, 30, 31, 110, 141, 51, 90, 109


CDKN2A
8, 31, 51, 133, 140, 167, 109, 110, 118


CDKN2A_ARF
31, 51, 110, 133, 180


CDKN2B
31, 110, 133, 167


CDKN2C
8, 31, 94, 122, 133, 109, 112, 118


CDKN2D
31, 109, 110, 167


CDPD1
60


CDR2
31


CDSN 
155


CDW52
109, 123, 160, 174


CDX1
51, 106


CDX2
51, 106, 151


CDY1
102 


CEACAM1
31, 51, 79, 154, 90, 110, 118


CEACAM5
31, 51, 110, 133


CEACAM6
31, 51, 109, 133


CEACAM8
135, 157, 160


CEBPA
31, 90, 109, 110


CEBPB
31, 51, 92


CEBPE
109


CENPF
31, 90


CES2
51


CETP 
53, 64, 105, 132


CFLAR
93, 109, 112, 118, 122, 123


CFM1
58


CFTR
18, 32, 58, 102, 141


CGA
30, 31, 70, 110, 150


CGB
31, 110, 133


CGB5
30, 110


CGB7
110


CGB8
30, 110


CHAT 
8, 10, 124


CHD3
63


CHD4
63


CHEK2
31, 51, 110, 154, 167


CHGA
110, 133, 167


CHGB
36, 110, 167


CHI3L1
31, 160


CHK
31, 51, 166


CHL1
162


CHRM1
8, 144, 162


CHRM2
8, 18, 62, 162, 169


CHRM3
8, 18, 51, 154


CHRM4
8, 18, 144


CHRNA1
124


CHRNA3
82


CHRNA4
8, 24, 82, 144


CHRNA5
82


CHRNA7
8, 24, 144, 162


CHRNB1
124


CHRNB2
82, 162


CHRNE
124


CHRNG
124


CHST2
51


CHUK 
31, 118, 154


CHX10
37


CIP29
35, 90, 109, 112


CIRH1A
47


CKB
8, 109, 127


CKMT1
93, 129


CLCA1
51


CLCN2
82


CLCN5
131


CLCNKB
98


CLDN1
31, 51


CLDN11
123


CLDN14
60


CLOCK
62


CLTCL1
112


CLU
8, 10, 31, 127, 154


CMD1B
129


CMD1C
129


CMD1E
129


CMD1F
129


CMD1H
129


CMD1J
129


CMD1K
129


CMH6
129, 144


CMKBR2
92


CMKBR5
92


CMM
118


CNK
110


CNN1
90


CNP
8, 70, 123


CNR1
31, 144, 154, 162


CNTF
8, 10, 122, 162


COCH
60


COL11A2
60


COL17A1
27, 91, 154


COL18A1
31, 35, 90, 112, 157, 109, 133


COL1A1
136


COL1A2
136


COL2A1
60, 135


COL3A1
14


COL4A1
154


COL4A2
154, 157


COL4A3
118


COL4A4
67


COL4A6
83, 154, 157


COL6A1
70, 129


COL6A2
129


COL6A3
129


COL9A3
129


COMP
160


COMT
23, 29, 31, 62, 144, 162


COPEB
154


COPS5
31, 150


CORTBP2
24


COX15
129


COX4I1
8


CP
8, 64, 105, 110, 132, 144


CPA5
24


CPB1
141


CPB2
127, 172


CPE
64, 105


CPI
49


CPLX1
29, 162


CPLX2
29, 162


CPT2
129


CPX
49


CR1
4, 47, 92, 123, 160, 110, 111, 122


CR2
18, 75, 92, 109, 111


CRABP1
42, 79, 109


CRABP2
166


CRAT
8


CREB1
8, 110


CREBBP
109


CREM
3, 94, 102, 111, 154


CRH
8, 110, 123


CRHBP
8, 57, 160


CRHR1
57


CRISP3
154


CRKL
109


CRMP1
110


CRYAA
37


CRYAB
8, 37, 75, 123, 129


CRYBA1
37


CRYBB1
37


CRYBB2
37


CRYGC
37


CRYGD
37


CRYGS
37


CRYM
60


CS
8, 47, 64, 132


CSE1L
31, 51, 109


CSEN 
8


CSF2
4, 31, 51, 166, 167, 92, 110, 133


CSF3
4, 31, 64, 133, 167, 92, 110, 132


CSH1
31, 70, 85


CSH2
31


CSK
154


CSN2
64, 105


CSPG2
31, 109, 118, 154


CSRP3
129, 154


CST
90, 157


CST3
8, 9, 10, 123, 51, 53, 110


CST6
31


CSTA
31, 154


CSTB
51, 82


CTAA1
37


CTAA2
37


CTAG1
51, 83, 110, 157, 112, 118, 122


CTAG2
30, 118, 133, 154


CTGF 
31, 47, 64, 109, 65, 103, 105


CTLA4
1, 18, 38, 174, 123, 124, 160, 105, 111, 122, 64, 92, 93


CTM
37


CTNNA1
51, 152


CTNNB1
31, 51, 90, 110, 133


CTNNBIP1
51, 118


CTNND1
30, 51, 118, 133, 154


CTNND2
154


CTPP
37


CTPP3
37


CTPS
109


CTSB
8, 31, 51, 110, 123, 133


CTSD
8, 31, 51, 92


CTSE
8


CTSG
8, 41, 56, 127, 172, 180


CTSH
110, 154


CTSK
135


CTSL
22, 31, 51, 76, 83, 118


CTSL2
31, 51, 157


CTSS
8, 70, 110


CTSW
109


CUBN
117


CUL2
157


CUTL1
31, 109


CX3CL1
56, 77, 92, 160


CX3CR1
4, 92


CXADR
30, 154


CXCL1
56, 74, 104, 166, 155, 160, 118, 135, 154


CXCL10
31, 51, 77, 133, 92, 110, 123


CXCL12
4, 31, 52, 154, 160, 106, 109, 112,



61, 90, 92


CXCL13
160


CXCL2
74, 118


CXCL5
74, 110, 126, 133, 160


CXCL9
5, 58, 88, 123


CXCR3
109, 123


CXCR4
31, 52, 91, 160, 170, 92, 154, 157


CXCR6
92


CXorf6
129


CYLD 
157, 166


CYP11A1
3


CYP11B2
98


CYP19A1
31, 79, 90, 154


CYP1A1
27, 31, 51, 110, 154, 157, 79, 83, 88


CYP1A2
51, 88, 141, 162


CYP1B1
31, 51, 83, 110, 154, 166


CYP21A2
1, 64, 105


CYP27A1
154


CYP27B1
42, 51, 154


CYP2A6
51, 83, 110


CYP2C19
30, 154


CYP2C9
45, 88, 110


CYP2D@
144


CYP2D6
10, 11, 27, 162, 88, 110, 144, 30, 31, 62


CYP3A4
90, 92, 109, 154


CYP46A1
8


CYP7A1
44


CYP7B1
88


CYR61
31, 133


D12S2489E
59


D2S448
118, 166


DAB1
162


DAB2
31, 154


DAB2IP
154


DAF
4, 42, 51, 114, 123, 109, 110, 112


DAO 
162


DAPK1
30, 31, 51, 133, 176, 109, 110, 112


DAZ
102


DAZL
102


DBCCR1
30, 176


DBH
23, 29, 162


DBI
8, 47, 162


DBN1
8, 70


DBP
87


DCC
51


DCK
70, 109, 154


DCN
31, 51


DCR
70


DCT
118


DCTD
109


DCX
82


DDB1
88, 113


DDB2
88


DDC
23, 24, 29, 167, 133, 144, 162, 36, 64, 105


DDIT3
31, 133


DDR1
31


DDX10
109


DDX26
110, 133


DDX6
51, 112


DEK
109, 111


DES
4, 110, 129, 167


DEXI
76


DFFB
31


DFN2
60


DFN4
60


DFN6
60


DFNA16
60


DFNA18
60


DFNA2
60


DFNA23
60


DFNA24
60


DFNA25
60


DFNA30
60


DFNA4
60


DFNA44
60


DFNA49
60


DFNA5
60


DFNA52
60


DFNA7
60


DFNB13
60


DFNB14
60


DFNB15
60


DFNB17
60


DFNB20
60


DFNB26
60


DFNB27
60


DFNB31
60


DFNB33
60


DFNB38
60


DFNB39
60


DFNB40
60


DFNB5
60 


DFNM1
60


DHCR24
8


DIA1
133


DIABLO
154


DIAPH1
60


DIO2
150


DIRC2
157


DISC1
29, 62, 162


DISC2
162


DJ1
144


DKK3
133


DLAT 
47


DLD 
128


DLEC1
83, 110


DLEU1
109


DLEU2
109


DLGAP2
82


DLST 
8


DMBT1
51, 83, 110, 133, 154, 167


DMD
129 


DMT1
61


DNASE1
58, 111


DNMT1
30, 31, 51, 176, 152, 154, 157, 88, 90, 110


DNMT3B
30, 51, 88, 133, 157, 167, 90, 109, 110


DNTT
109


DOK1
109


DP1
152


DPH2L1
31


DPM3
154


DPP4
4, 51, 64, 154, 161, 92, 118, 132


DPYD
30, 31, 51, 83, 106, 157


DPYSL5
110


DRD1
8, 29, 98, 144, 162


DRD2
8, 110, 162, 167


DRD3
23, 29, 73, 144, 162


DRD4
12, 23, 29, 144, 162


DRD5
23, 24, 29, 144, 162


DSC3
31


DSCAM
70


DSCR1
8, 70


DSCR3
70


DSCR5
70


DSCR8
70, 118


DSG1
83


DSP
31, 129


DSPP
60


DSTN
8


DTNBP1
162


DTR
51, 68, 110, 122, 134, 154


DTYMK
31


DUSP1
30, 31, 51, 154


DUT
51


DYRK1A
70


DYSF
129


DYT1
144


DYT3
144


DYX1
73


DYX2
73


DYX3
73


DYX5
73


DYX6
73


E2F4
31, 51, 79, 109, 154, 180


EB-1
109


EBAG9
30, 31, 83, 133, 140


EBNA1BP2
75


ECA1
82


ECE1
51, 79


ECGF1
30, 31, 51, 129


ED1
118, 166


EDN1
110


EDN2
98


EDNRA
31, 42, 51, 132, 134, 174, 64, 98, 108


EEC2
48


EEF1A2
31


EEF2
8, 31


EFMR
82


EFNA1
31, 51, 110, 118, 157


EFNB2
51


EGF
31, 110, 133


EGFR
31, 51, 110, 133, 167


EGI
82


EGI14
82


EGR1
8, 31, 110, 133


EIF2S1
8, 31, 110, 118


EIF3S3
31, 154


EIF3S6
31, 133


EIF4A1
90, 118


EIF4A2
88, 112


EIF4E
31, 51, 110


EIM
82


EJM1
82


EJM2
82


ELAC2
154


ELAVL2
133, 167


ELAVL3
77


ELAVL4
167


ELF3
31, 110, 154


ELL
109


ELN
110


ELOVL4
113


EMP1
31


EMS1
31


ENC1
51


ENFL2
82


ENG
31, 51, 110, 118, 133, 154


ENO1
31, 110, 111


ENO2
31, 110, 133, 167


ENO3
110


ENPEP
8, 157


ENPP1
64, 132


ENPP2
110, 118, 133, 160


ENTPD1
93, 109, 112, 118


ENUR1
81


ENUR2
81


EP300
31, 51, 109


EPAS1
30, 31, 133, 157


EPB41
114


EPB41L3
133


EPD
82


EPHA2
31, 51, 110, 157, 118, 133, 154


EPHA3
118, 133, 157, 167


EPHA4
31


EPHB2
167


EPHX1
30, 46, 76, 90, 110


EPM2A
82


EPO
4, 31, 92, 110, 133, 167


EPOR
31, 109


EPPS
82


EPS15
109


EPX
18, 31, 78, 180


ERBB2
26, 30, 31, 154, 167, 176, 51, 110, 133


ERBB3
31, 51, 110, 154, 166, 118, 133, 140


ERBB4
31, 51, 154


ERCC1
42, 51, 109, 133


ERCC2
27, 83, 110, 118


ERCC5
110


ERCC6
110


EREG 
30, 51, 140, 154


ERG 
42, 109


ERN1
8


ERN2
103


ERVWE1
4, 8, 92, 123


ESR2
31, 110


ESRRA
31


ETS1
31, 51, 110


ETS2
31, 42, 51, 70, 90, 154


ETV4
31, 110, 133


EVI1
109


EVPL
83


EXO1
51


EXTL3
31, 51


EYA1
37, 60


EYA4
60


EZH2
109, 112, 154


F10
172


F11
109, 127, 172


F12
88, 172


F13A1
48, 49, 56


F2
8, 31, 51, 133, 64, 105, 132


F2R
31, 172


F2RL1
31


F3
4, 8, 31, 133, 51, 64, 132


F5
53, 103, 127, 168, 172


F7
64, 127, 132, 172


F8
87


F9
87


FAAH 
31


FABP1
154


FABP2
53, 64, 97, 105, 132, 134


FABP3
31, 127


FABP4
30, 176


FABP5
30, 155


FABP7
31


FACL4
51


FADD 
51, 64, 105, 133


FADS1
134


FADS2
31, 109, 113


FANCA
31


FAP
118


FASN
31, 51, 110, 152, 154, 180


FBL
90, 160


FBLN5
31, 51, 112, 157


FBN1
14


FBN2
14


FBP1
64, 132


FBXW7
31, 79


FCAR 
18, 92


FCER2
18, 20, 88, 123, 160, 92, 109, 111


FCGR1A
112


FCGR2A
123


FCGR2B
111, 112, 118


FCGR3A
4, 111


FCGR3B
18, 111, 161, 171


FDXR
51


FES
31, 109, 110, 112, 118


FGA
9, 21, 172


FGB
52, 53, 98, 127, 146, 172


FGF1
31, 53, 64, 109, 154


FGF3
31, 110, 167


FGF5
31, 154, 157


FGF6
154


FGF8
31, 154


FGFR1
8, 31, 51, 133


FGFR2
30, 31, 79, 154


FGFR3
30, 42, 51, 109, 122, 176


FGFR4
31, 51, 150


FGG
172


FGL2
88


FH
157


FHIT
31, 42, 110, 133


FHL2
31, 154


FIGF
31, 51, 110


FIMG1
124


FKBP1A
92


FKBP1B
186


FKBP4
31


FKBP5
154


FLG
155, 160


FLJ11383
51


FLJ14813
171


FLJ22795
51, 110


FLT1
31, 51, 110, 133


FLT3
109


FLT3LG
16, 109, 111, 112, 157, 160


FLT4
31, 51, 90, 133, 154, 109, 110, 112


FMR1
24, 84


FMR2
84


FN1
31, 51


FOLH1
154


FOLR2
109


FOS
8, 31, 92, 110, 123, 133


FOSB
31


FOSL1
31, 42, 51, 83, 110, 167


FOSL2
31


FOXA2
64, 132


FOXN1
6


FOXP3
64, 105


FPEVF
82


FPGS
51, 109


FPR1
92


FPRL1
8


FRAT1
31, 42, 83


FRDA
64, 132


FRK
31


FRZB
31


FSHB
30, 92, 102, 150


FSHR
102


FST
107, 150


FTH1
31


FTL
8, 37, 144


FURIN
31, 51, 92, 110


FUS
109


FUT1
51


FUT3
51


FUT4
110


FUT7
110, 133


FUT8
51, 138


FVT1
112


FXYD3
31


FY
114, 162


FYN
92, 109, 112, 157


FZD10
51


FZD5
109, 160


G22P1
30, 31, 42, 109, 111


G6PC
64, 132


G6PD
8, 31, 51, 64, 86, 132


G72
162


GABBR1
82


GABRA1
82


GABRA3
29, 47, 82, 123


GABRA5
29


GABRB3
24, 29, 49


GABRG2
82


GABRG3
24


GAD1
8, 64, 82, 105, 144, 162


GAD2
64, 66, 82, 174, 105, 132, 162


GADD45A
109, 110, 118


GADD45B
110


GADD45G
109, 110


GAL
8, 12, 57, 134, 150


GALK1
37


GALNT3
31, 51


GALT
79


GAP43
8, 10, 29, 62, 162


GAPD
8, 31, 51, 64, 105


GARP
31


GAS
51, 64, 132


GAS6
160


GASC1
83


GATA1
70, 171


GATA2
109


GATA3
31, 60, 92


GBX2
154


GC
64, 105, 123, 132


GCGR 
64, 85, 98, 105, 132


GCK
64, 132


GCKR
64, 132


GCLC
51, 86, 109


GCNT2
37


GCSH
96


GFAP
4, 8, 123


GFPT1
64, 132


GFRA1
116


GFRA2
116


GFRA3
116


GGH
109


GHR
12, 31, 47, 107, 134, 154, 64, 90, 105


GHRHR
110, 150


GHRL
12, 64, 132, 134, 150, 154


GIPC2
51, 157


GIPR
57


GJA3
37


GJA4
31, 110


GJA8
37


GJB1
51


GJB2
30, 31, 60, 155, 79, 90, 118


GJB3
60


GJB6
60


GLDC 
96


GLI
27, 112


GLI2
27


GLP1R
64, 132


GLUL
8, 90, 123


GNA11
150


GNAI2
110, 150, 186


GNAL 
29, 162


GNAO1
8


GNAQ 
8, 150


GNAS 
57, 150, 154


GNAT2
113


GNB3
8, 29, 53, 127, 132, 134, 64, 65, 98


GNE
129


GNMT 
90


GNRH2
31, 79


GNRHR
118, 154


GOLGA5
173


GOLGB1
92, 160


GP9
171


GPA33
51


GPC1
31


GPC3
31, 90


GPD2
64, 132


GPI 
86, 160


GPR1
92


GPR15
4, 92


GPR2
5, 20, 118, 155


GPR30
31


GPR37
109


GPR44
20, 92


GPRK5
91, 98, 160


GPT
47, 88


GPX1
86, 110, 154


GPX4
102


GRB2
8, 31, 109


GRB7
31, 83


GRIA1
8, 77, 82, 162


GRIA2
8, 77, 82, 162


GRIA3
29, 77, 82


GRIA4
8, 77, 82


GRIK1
10, 70, 77, 82


GRIK2
82


GRIK3
77, 162


GRIK4
82, 162


GRIK5
82, 162


GRIN1
8, 10, 29, 62, 82, 162


GRIN2B
8, 77, 162


GRM2
162 


GRM3
29, 162


GRM5
10, 162


GRM7
162


GRN
31


GRP
51, 71, 83, 110, 154, 167


GRP58
102


GRPR
31, 51, 110, 154


GSBS
95


GSE
38


GSK3A
90


GSN
9, 30, 31, 154, 58, 110, 133


GSR
8, 31, 51, 110, 167, 64, 86, 105


GSS
86


GSTA1
30, 51, 57, 154


GSTA2
31


GSTM1
31, 110, 133, 167


GSTM3
18, 27, 31, 51, 110, 123


GSTP1
31, 110, 133, 167


GSTT1
30, 31, 51, 110


GUCA2A
51, 106


GUCA2B
51, 151


GUCY2C
51, 83


GUSB
8, 31, 51, 110


GYPC
114


GYS1
64, 132, 134


GZMA
75, 92, 160


GZMB
31, 92


HADH2
8


HADHA
186


HAGH
157


HARS
92


HAS1
122


HAS2
154


HAS3
154


HBA1
7, 64, 105


HBA2
7, 163


HBB 
28, 114, 163


HBD
163


HBG1
28


HBG2
28, 163


HBZ
7, 28


HCK
92, 109


HD
8, 51


HDAC1
31, 109


HDGF
83, 90


HDPA
93


HES1
31


HF1
30, 160


HFE
28, 47, 64, 88, 105, 144


HGFAC
51


HIC1
31, 51, 83, 133, 109, 110, 112


HIP1
51, 109, 154


HIST4H4
31, 84, 111


HK1
64, 86, 132


HK2
64, 132, 134


HLA-A
51, 64, 83, 118, 157, 162, 88, 92, 105


HLA-B
4, 8, 92, 123


HLA-C
42, 51, 64, 156, 118, 123, 155, 83, 92, 105


HLA-DMB
64, 105, 123, 160


HLA-DPB1
38, 48, 64, 123, 124, 160, 93, 105, 109


HLA-DQA1
64, 105, 132


HLA-DQB1
64, 105, 123, 132


HLA-DRA
123


HLA-DRB1
64, 88, 105, 160, 174, 111, 123, 156


HLA-DRB3
51, 56, 64, 123, 132, 92, 105, 111


HLA-DRB4
38, 47, 109, 125


HLA-DRB5
64, 105, 109, 123


HLA-E
59, 64, 77, 105, 123


HLA-G
92, 109, 112, 118, 157, 166


HLF
109


HLXB9
109


HMBS
26, 83, 112


HMGA1
31, 51, 110


HMGA2
79, 110


HMGB1
31, 90, 180


HMGCR
8, 31, 51, 132, 64, 95, 110


HMMR
31, 51, 109, 112, 122


HMOX1
8, 123, 127, 144, 157


HMOX2
155


HN
8


HNF4A
64, 90, 132


HNMT
18, 70, 72, 161, 162


HNRPA1
92, 109


HNRPA2B1
83, 92, 110, 167, 111, 133, 160


HOXA1
24, 31, 110


HOXA10
102, 109, 133


HOXA11
109, 171


HOXA13
109


HOXA3
109


HOXA4
109, 157


HOXA5
109


HOXA6
109


HOXA7
109, 110


HOXA9
109


HOXB2
109


HOXB3
109


HOXB4
109, 157


HOXB5
109, 157


HOXB6
51, 109


HOXB7
31, 109


HOXB8
51


HOXB9
157


HOXC11
157


HOXC4
27, 157, 166


HOXC5
42, 112


HOXC8
42, 51


HOXD11
109


HOXD13
109


HOXD3
110


HOXD4
157


HOXD8
64, 105


HP
31, 64, 92, 105, 141


HPCQTL19
154


HPCX
154


HPN
154


HPRT1
107, 109, 110, 118, 123


HPSE
83


HR
6


HRAS 
30


HRASLS
31, 110, 118, 157


HRC
64, 132


HRG
4, 18, 46, 107, 127


HRH1
8, 18, 183


HRH2
8


HRH3
144


HSAJ2425
31, 109


HSD11B1
134


HSD11B2
3, 98


HSD17B1
31, 51, 154


HSD17B2
51, 79, 154


HSD17B3
154


HSD3B1
98, 154


HSD3B2
154


HSD3B7
45


HSF1
31, 154


HSF4
37


HSPA5
31, 51, 160


HSPA8
8, 31, 100


HSPB1
8


HSPCA
31, 112


HSPCB
31, 111


HSPD1
8, 64, 105


HSPG2
8, 31, 110, 133


HT
174


HTNB
98 


HTR1A
8, 29, 62, 64, 132, 162


HTR1B
110, 120


HTR1D
120


HTR1F
73, 120


HTR2A
8, 12, 23, 120, 162, 24, 29, 62


HTR2B
120


HTR2C
29, 120, 162


HTR3A
29, 162


HTR6
8, 29, 162


HVEC
4


HYAL1
154


HYAL2
110, 133, 167


HYMAI
64


HYPLIP1
97


HYPLIP2
97


HYT1
98


HYT2
98


HYT3
98


IAPP 
9, 58, 64, 132, 134


IBMPFD
61, 129, 139


IBSP
31, 51, 110, 122, 154


ICA1
64, 105


ICAM2
56, 92, 160, 180


ICAM3
56, 92, 93, 160, 174, 180, 111, 112, 123


ID1
31, 42, 79, 154, 83, 118, 141


IDDM1
64, 105


IDDM10
64, 105


IDDM11
64, 105


IDDM12
64, 105


IDDM13
64, 105


IDDM15
64, 105


IDDM17
64, 105


IDDM18
64, 105


IDDM2
64, 105


IDDM3
64, 105


IDDM4
64, 105


IDDM5
64, 105


IDDM6
64, 105


IDDM7
64, 105


IDDM8
64, 105


IDDMX
64, 105


IDE
8, 64, 132


IDS
84


IFNA1
4, 79, 88, 157, 92, 109, 118


IFNA2
51


IFNB1
4, 31, 51, 123, 133, 110, 115, 118, 77, 91, 92


IFNG
31, 42, 51, 178, 110, 133, 167


IFNGR1
47, 92, 111, 114, 125, 178


IFNGR2
125


IGES
18


IGF1
31, 51, 60, 133, 105, 110, 132, 64, 67, 92


IGF1R
31, 110, 118, 154


IGF2
4, 8, 31, 110, 132, 51, 64, 105


IGF2R
31, 51, 90, 110


IGFALS
47, 64, 105


IGFBP1
31, 51, 64, 105, 132


IGFBP2
31, 51, 64, 134, 105, 110, 132


IGFBP4
31, 51, 64, 154, 107, 110, 132


IGFBP5
31, 42, 64, 154, 79, 105, 107


IGFBP6
133, 154


IGFBP7
31, 154


IGSF4
31, 90, 110, 133, 154


IKBKB
64, 132


IL10
4, 8, 31, 133, 178, 110, 112, 123, 92, 105, 106, 35, 



51, 64


IL10RA
133, 155


IL12A
20, 56, 92, 118, 123, 154


IL12B
64, 92, 105, 123, 154


IL13
4, 18, 31, 105, 123, 159, 51, 64, 92


IL13RA1
93, 175


IL13RA2
18, 175


IL15
31, 92, 110, 167


IL16
18, 56, 92, 112, 160


IL18
31, 51, 64, 92, 105, 123


IL1A 
4, 8, 31, 133, 105, 110, 123, 75, 90, 92, 51, 61, 64


IL1B 
31, 110, 167


IL1R1
64, 105, 135


IL1R2
135


IL1RL1
111


IL1RN
4, 8, 31, 132, 167, 110, 118, 123, 64, 92, 105


IL21R
112


IL24
104, 110, 118, 133


IL2RA
31, 51, 64, 133, 155, 167, 92, 105, 123


IL2RB
92, 109, 110, 118, 162


IL2RG
56, 77, 123


IL3
4, 8, 31, 109, 123, 133


IL3RA
92, 109


IL4
4, 8, 31, 133, 105, 110, 123, 51, 64, 92


IL4R
18, 64, 105, 112, 123, 157


IL5
31, 64, 92, 133, 105, 110, 123


IL6R
4, 31, 42, 127, 150, 112, 122, 123, 56, 77, 92


IL6ST
4, 8, 31, 92, 110, 133


IL7
51, 92


IL7R
92, 109


IL8
4, 31, 51, 110, 123, 133, 64, 92, 105


IL8RA
59


IL8RB
4, 92, 154, 155, 178


ILK
31, 65, 152, 154


ILVASC
6


IMP-1
31, 51


IMP-2
47, 90


INA
109, 112


ING1
31, 83, 118


INHBB
102


INPPL1
64, 132


INS
8, 64, 85, 132, 134, 92, 98, 105


INSM1
110


INSR
8, 31, 64, 132, 134, 85, 105, 129


IPF1
64, 132


IRF1
110, 133


IRF2
123


IRF4
122


IRS1
64


IRS2
31, 64, 85, 132, 134


IRTA1
112, 122


ISGF3G
31, 109, 118


ISL1
64, 132, 134


ITGA11
133


ITGA2
31, 51, 110, 127, 169, 171


ITGA2B
53, 64, 127, 154, 171


ITGA3
31, 51, 79, 118, 154


ITGA4
31, 92, 123


ITGA5
35, 51, 90, 133, 118, 155, 109, 112, 122 


ITGA6
27, 31, 51, 175, 154, 160, 166, 90, 110, 142 


ITGA7
129


ITGA9
110, 133, 167


ITGAL
4, 51, 92, 123


ITGAM
4, 8, 31, 92, 123


ITGAX
92


ITGB1
4, 31, 51, 167, 110, 123, 133, 64, 92, 105 


ITGB2
92, 123


ITGB3
40, 41, 51, 172, 127, 154, 171, 102, 111, 118, 53, 



67, 92


ITGB5
31


ITGB7
64, 105, 109, 112, 122


ITM2B
61


IVL
31, 42, 75, 155, 83, 110, 133


IVNS1ABP
104


JAG1
42, 60


JAG2
42, 83, 122


JAK1
31, 122, 154, 157


JAK2
31, 51, 109, 154, 122


JAK3
20, 109, 112, 157


JRK
82


JUN
8, 31, 51, 110, 123, 133


JUNB
31, 92, 93, 109, 112


JUP
31, 51, 118, 133


KAI1
30, 31, 42, 133, 154, 51, 83, 110


KCNA1
31


KCNA5
21


KCNE1
21


KCNH1
31, 42


KCNJ11
64, 132


KCNJ2
21


KCNJ3
31, 64, 132


KCNJ6
64, 70, 132


KCNJ8
53


KCNJ9
64, 132


KCNN3
29, 162


KCNN4
58


KCNQ1
21, 60


KCNQ2
82


KCNQ3
82


KCNQ4
60


KIAA1199
60


KIR2DL1
92, 155


KIR3DL1
4


KISS1
31, 118


KIT
31, 51, 92, 167, 109, 110, 183


KITLG
31, 51, 92, 110, 133, 167


KL
107, 136, 157


KLF1
28


KLF4
31, 51, 152


KLF5
31, 53, 154


KLHL4
49


KLK1
79, 98, 141


KLK10
31, 154


KLK11
154


KLK13
31


KLK2
154


KLK3
31, 107, 154


KLK4
154


KLK5
31, 154


KLK6
8


KLK8
8


KLKB1
107


KLRB1
123


KLRC1
92, 118


KLRD1
59, 92, 102, 118


KRAS2
51


KRT13
30, 42


KRT14
31, 110


KRT17
42


KRT18
31, 47, 110, 133


KRT20
31, 51, 110, 154


KRT7
31, 45, 47, 110


KRT8
47


KRTHB1
31


L1CAM
49, 118


LAF4
109


LAMA1
8, 51, 67, 110


LAMA3
110


LAMA5
110


LAMB1
51, 154


LAMB2
154


LAMB3
133, 154


LAMC2
51, 83, 133, 166


LAMP1
51, 118


LAMP2
51, 118


LAMP3
31, 51, 83


LAMR1
31, 51, 110, 118, 133


LASP1
31


LAT
160


LBP
133


LCAT
64, 95, 97, 132


LCK
51, 64, 75, 167, 109, 110, 157, 83, 92, 105


LCN1
58, 110


LCN2
17, 51, 56, 69, 103, 180


LCO
90


LCP1
31, 112, 154


LCS1
45


LDHA
31


LDLR
51, 64, 95, 110, 132


LEF1
51, 112, 118


LEP
31, 64, 85, 133, 134, 92, 105, 132


LEPR
12, 31, 33, 134, 109, 150, 105, 64, 92, 110


LGALS1
30, 31, 51, 110, 154


LGALS3
31, 51, 110, 133


LGALS3BP
31, 88, 92, 133, 106, 110, 112


LGI1
82


LHX2
109


LIG4
31, 109, 122


LILRB1
59, 92


LILRB2
160


LIM2
37


LIPC
53, 64, 97, 105, 132


LIPE
64, 97, 132, 134


LMNA
21, 31, 42, 129, 133, 154, 51, 83, 110


LMNB1
31, 42, 51, 83, 133, 154


LMO1
109


LMO2
109, 110


LMOD1
174


LOC90925
109


LOH11CR2A
31, 110


LOR
142


LOST1
110


LOX
31


LPA
8, 52


LPL
8, 64, 105, 132


LPP
109, 110


LRP1
8, 31, 53, 118, 154


LRP2
8


LRP5
64, 105, 136


LRPAP1
8


LTA
31, 51, 64, 127, 110, 132, 105, 92, 123 


LTB
47, 88, 160


LTB4R
92


LTC4S
18, 109, 165


LTF
4, 8, 31, 92


LUC7L
7


LUM
31, 42


LY75
31


LYL1
109


LYN
35, 51, 109, 112


LYZ
9


LZTS1
31, 83, 133, 154


MAD
110, 166


MAD1L1
112, 154


MAD2L1
31, 109, 112


MADCAM1
56, 103, 109, 112, 180


MADH1
31, 152


MADH3
31, 51, 56, 83, 152, 180


MADH4
31, 110, 133, 140, 151


MADH5
51, 109


MADH6
90


MADH7
56, 90, 180


MAF
37, 122


MAG
24, 123


MAGEA10
118


MAGEA3
30, 31, 110, 118


MAGEA4
83, 110, 118


MAGEC1
118


MAGEE1
118


MALT1
110, 112, 166


MAOA
8, 13, 23, 144, 162, 24, 29, 62


MAOB
8, 10, 23, 162, 24, 29, 144


MAP1B
8


MAP2
8, 82, 118, 144, 162


MAP2K1
8, 31, 51, 110


MAP2K3
46, 137, 154


MAP2K4
31, 51, 154


MAP2K5
154


MAP2K6
8


MAP3K1
79, 154


MAP3K3
90


MAP3K4
31


MAP3K8
31


MAP4
31


MAPK1
31, 51, 110


MAPK10
8


MAPK11
154


MAPK14
31, 51, 64, 132


MAPK3
8, 31, 51, 92, 133, 167


MAPK6
154


MAPK8
31


MAPK8IP1
64


MAPKAPK2
31


MAPKAPK3
110


MAPT
8, 61, 70, 144


MAT1A
90


MAT2A
90


MATK
31


MATN3
135


MAX
31


MAZ
135


MBD1
51, 110


MBD2
31, 51, 154


MBD4
51


MBL2
4, 58, 88, 92, 114, 163


MBP
4, 8, 24, 61, 123


MC1R
27, 118, 154, 166


MC2R
3


MC3R
134


MC4R
12, 33, 134


MCC
31, 51, 83, 110, 152


MCP
91, 110, 123


MDK
8, 51, 71, 106, 110


MDM1
60


MDM2
31, 51, 110, 133


MDS1
109


ME1
31


MEAX
129


MEBA
82


MECP2
24, 133


MEF2A
52


MEFV
9


MEIS1
109


MEN1
31, 36, 110, 167


MEP1A
51


MEST
31, 51, 110


MET
90, 157


MFGE8
31


MFI2
8, 118


MGAT3
47, 90


MGAT5
51, 88, 90, 118


MGP
127


MGR1
120


MGR2
120


MGR3
120


MGR4
120


MGR5
120


MGR6
120


MGST1
110


MHC2TA
64, 77, 92, 123, 160, 167, 105, 110, 112 


MIA
51, 118, 157


MICA
1, 38, 56, 166, 178, 180, 64, 105, 155 


MIP
37


MIPS
127


MITF
60, 118


MJD
82, 144


MKKS
53 


MKL1
109


MLANA
110, 118, 157, 166


MLC1
61, 162, 184


MLF1
109


MLH1
31, 51, 103, 166, 110, 133, 151


MLH3
51


MLLT1
109


MLLT10
109, 112


MLLT2
109


MLLT3
109


MLLT4
109


MLLT6
109


MLLT7
109


MLN 
64, 66


MLN51
31


MME
8, 110, 133, 167


MMP1
31, 51, 110


MMP10
31, 51, 67, 166


MMP12
46, 51


MMP13
14, 31, 42, 160, 166, 83, 118, 135


MMP15
90


MMP16
118


MMP2
4, 8, 10, 144, 167, 123, 132, 133, 64, 110, 118, 31, 



51, 61 


MMP26
79, 110, 154


MMP3
31, 51, 56, 123, 167, 180


MMP8
118, 160


MMP9
31, 51, 110, 112, 133


MNT
31


MOBP
123


MOG
24, 123


MPD1
129


MPD2
129


MPG
31, 42, 102


MPL
171


MPO
8, 110, 123, 167


MPRM 
129


MPZ
112


MRE11A
31, 112


MRPL28
118


MRXE 
82


MS4A1
92


MS4A2
18


MSF
31, 109


MSH2
31, 51, 79, 151, 154, 106, 112, 13 8 


MSH3
31, 51, 79, 152, 109, 167, 83, 133


MSH6
51, 138, 151


MSLN
31, 42, 51, 79, 83, 110


MSMB
154


MSN
70, 92, 160


MSR1
8, 97, 154


MSSE 
27


MST1
110, 157, 167


MST1R
31, 51, 110, 133


MSX1
48, 49


MT1B
31


MT1E
31, 154


MT1X
30, 31, 154


MT2A
31, 135, 154


MT3
8, 31, 154


MTA1
31


MTAP 
109, 110, 133


MTATP6
88


MTBS1
178


MTBSX
178


MTCO2
8, 51, 100, 129


MTCP1
109


MTHFR
8, 31, 51, 132, 53, 64, 110


MTM1
129


MTND5
8, 129, 144


MTNR1A
8


MTP
95


MTR
51, 70


MTRR
70, 117


MUC1
31, 110, 133


MUC3A
56, 180


MUC4
26, 51, 106, 110, 133, 141


MUC5B
58, 110, 133


MUC6
26, 31, 51, 56, 110


MUC8
102, 110, 165


MUSK 
124


MVK
90


MX1
88, 104, 123, 143, 159


MXI1
154, 167


MYAS1
124


MYBL1
35, 109, 112


MYBL2
154


MYBPC3
129


MYCL1
30, 31, 42, 122, 133, 51, 83, 110


MYCN
110, 167


MYF6
129


MYH2
129


MYH6
100, 129


MYH7
100, 129


MYH9
60


MYL2
100, 129


MYL3
100


MYL4
127


MYLK2
129


MYO15A
60


MYO18B
110


MYO1A
60


MYO1G
109


MYO3A
60


MYO6
60


MYO7A
60


MYOD1
31, 51


MYST3
109


N33
51, 110, 154


NAP1
107


NBL1
31


NBS1
31, 109, 112


NCAM1
8, 24, 31, 133, 167, 51, 92, 110


NCAM2
70


NCF1
134


NCF2
8, 56, 64, 132


NCKAP1
8


NCL
92, 109, 111


NCOA1
31


NCOA2
31, 109, 154


NCOA3
31, 79, 109, 154


NCOA4
31, 154, 173


NCOR1
31


NCOR2
31, 109


NCSTN
8


NDP
60


NDRG1
51


NDUFV2
144


NEB
129


NEDD5
8, 109


NEF3
8, 10, 144


NEFH
10


NEFL 
8, 10, 31, 154, 70, 61, 123


NEK4
31


NES
118


NEUROD1
64, 105, 132


NEUROG3
64, 132


NF1
31, 51, 110, 118, 167


NFKB1
31, 92, 133


NFKB2
31, 109, 112, 122


NFKBIA
31, 51, 92, 110, 133


NFKBIL1
123, 160, 180


NGFB
8, 123, 154


NGFR 
8, 31, 92, 123, 144


NHLRC1
82


NID
67


NIDDM2
64


NIDDM3
64


NISCH
98


NKX3-1
154


NLGN3
24


NLGN4
24


NMB
51


NME1
31, 90, 110, 133


NME2
51, 110, 118


NMT1
30, 51, 92


NMTC1
173


NOL1
31, 51, 110, 154


NONO 
157


NOS1
8, 10, 18, 98, 144


NOS2A
4, 8, 31, 114, 132, 133, 98, 105, 110, 64, 88, 92, 51, 



58, 61 


NOS3
8, 31, 54, 64, 110, 132


NOTCH1
42, 51, 109, 167


NOV
3, 31, 154, 157


NP
18, 109, 112, 174


NPHP1
107


NPPA
64, 98, 105, 132, 167


NPPC
107


NPR3
51, 98


NPY
8, 31, 64, 92, 132


NPY2R
82


NPY5R
134


NQO1
8, 30, 31, 133, 154, 182, 51, 109, 110 


NR0B1
3


NR0B2
64, 132, 134


NR1I2
31


NR2C1
31, 142, 163


NR2F1
3, 57


NR2F2
3, 31, 57


NR2F6
31


NR3C1
4, 8, 31, 167, 110, 132, 134, 57, 64, 92 


NR3C2
57, 98


NR4A1
31, 110


NR4A2
29, 144, 162


NR5A1
3, 150


NRAS
51


NRG1
8, 31, 123, 154, 162


NRIP1
31


NRP1
154


NRP2
36


NSEP1
31, 133


NSF
162


NTF3
8, 10, 118, 154, 162


NTF5
10


NTRK1
8, 31, 116, 167, 173


NTRK2
8, 10, 154, 162


NTRK3
8, 109, 116, 157


NTS
8, 110, 144, 154, 162, 167


NUFIP1
84


NUMA1
51, 109


NUP153
80, 149


NUP214
92, 109


NUP88
31, 47, 51, 154, 90, 93, 110


NUP98
109


OADIP
135


OAS2
88, 109, 118, 122


OASD
60


OASF
135


OATL1
157, 171


OB10P
134


OB10Q
134


OB4
134


OCLN
56, 74, 92, 180


OGDH 
8


OGG1
51, 83, 110, 133, 154, 157


OGT
51


OLIG2
109


OLR1
8, 172


OMG 
24, 123


OPHN1
51


OPLAH
110


OPRD1
8, 92, 144


OPRK1
8, 92


OPRM1
8, 144


OQTL 
134


OR51E2
154


ORC5L
109


ORM1
31, 110


ORM2
31, 110


OSM
31, 92, 110, 154, 118, 122, 133


OSMR
31


OTOA
60


OTOF
60


OXT
4, 110, 123, 167


OXTR
31


P2RX7
109


P2RY12
172


P2RY2
58


P8
31, 141


PABPC1
55


PACE4
31, 92, 110


PADI4
160


PAEP
79, 102


PAH
162 


PAK1
31


PAM
110, 123, 154


PAPPA
53, 70


PARK10
144


PARK11
144


PARK2
61, 144


PARK3
144


PARK4
144


PARK6
144


PARK8
144


PARK9
144


PAWR
8, 10, 144, 154, 157


PAX2
157


PAX3
60, 118


PAX4
64, 132


PAX5
112 


PAX6
30, 37, 51, 64


PAX7
110


PBCA
64, 105


PBOV1
30, 31, 51, 110, 154


PBP
154


PBX1
109


PCAF 
31


PCAP
154


PCBC
154


PCBD
51


PCC
37


PCK1
64, 132


PCM1
173


PCMT1
8, 37


PCNA 
8, 31, 51, 133


PCSK1
31, 64, 92, 150, 167, 110, 132, 134


PCSK2
24, 64, 110, 132, 167


PCSK7
112 


PCSK9
95


PDB 
139


PDB3
139


PDB4
139


PDCD1
111


PDCD8
112, 133


PDE4D
168


PDE5A
30, 176


PDGFA
31


PDGFB
31, 51


PDGFRA
27, 106, 109, 166


PDGFRL
51, 89, 90, 133, 154


PDPK1
64, 132


PDYN 
24, 29, 46, 62, 162


PEA15
64, 132


PECAM1
31, 47, 56, 163, 174, 180, 135, 157, 160, 123, 127, 



133, 109, 110, 118


PEPD 
31


PFC
119


PFKL
29, 86


PFKM 
64, 132


PFN1
31


PGA5
22, 145


PGAM2
129


PGC
31, 145


PGF
51, 70, 110, 118, 157


PGGT1B
30, 31, 110


PGK1
16, 86, 144


PHB
31


PHF11
18


PHKA1
109


PI
47, 76


PI3
31, 128, 155


PIAS3
112


PICALM
109


PIGR
51, 110


PIK3CA
42, 110, 133, 138


PIK3R1
31, 51, 64, 93, 132


PIM1
112, 154


PIN1
8


PIP
31, 139


PITPNM1
113


PITX3
37


PKD1
31


PKLR 
64, 132


PKM2
31, 51, 106, 157, 110, 133, 142


PLA2G10
51


PLA2G2A 
51, 118, 141, 152, 154


PLA2G7
4, 18, 41


PLAB 
31, 154


PLAGL1
31, 64


PLAT 
31, 51, 64, 133, 152, 123, 132, 134, 92, 105, 110


PLAU 
8, 31, 51, 133, 152, 92, 110, 123


PLAUR
31, 51, 92, 110, 123, 133


PLCB1
167


PLCB3
36


PLCD1
8, 29, 51, 54, 152


PLCG1
29, 31, 51, 152


PLCL1
110, 133, 167


PLD1
31, 51


PLD2
31, 51, 157


PLEC1
92, 154


PLK
51, 83, 110, 112, 133


PLP1
123


PLTP
64, 76, 105, 146, 132, 134


PLU-1
31


PMS1
51, 151


PMS2
51, 79, 118, 151, 154


PNCA1
140


PNMT
8, 98, 144


PNOC
162


POLB
30, 31, 51, 109, 110, 154


POLG
102


POLK 
133


POMC 
4, 8, 31, 167, 132, 110, 123, 134, 64, 92, 105


PON1
41, 52, 53, 132, 105, 144, 95, 64, 127


PON2
41, 52, 53


POR
3, 31, 110


POU3F4
60


POU4F3
60


PPARA
30, 64, 97, 132, 154


PPARD
51, 95


PPARGC1
64, 132, 134


PPID
31, 154


PPM1D
31, 154


PPND
61, 144


PPP1CC
31


PPP1R15A
118


PPP1R3A
51, 64, 132, 133, 167


PPP2CB
31


PPP2R1B
31, 51, 110


PRCC
157


PRDM2
31, 51, 79, 90, 110, 112


PRDX1
8, 70, 109


PREP
8


PRF1
14, 51, 88, 92, 122, 123


PRG2
18, 174


PRKAA2
64, 132


PRKAG2
129, 144


PRKAR1A
31, 57, 111, 150, 154, 173


PRKCA
8, 31, 51, 150, 64, 110, 132


PRKCD
154, 157


PRKCE
8, 31, 51, 154, 167, 92, 110, 133


PRKCG
8, 31, 51, 154


PRKCL1
8


PRKCM
31, 110, 167


PRKCQ
64, 109, 132, 134


PRKCZ
8, 31


PRKDC
51, 109


PRKN
144


PRKR
8, 31, 51, 118, 187, 91, 92, 109


PRL
4, 12, 31, 105, 111, 123, 51, 64, 92


PRLR
31, 150, 154


PRM1
102


PRM2
102


PRND 
8


PRNP 
8, 61


PRODH
162


PROM1
109


PROMM
129


PROS1
172


PROZ 
41


PRSS1
51, 141


PRSS2
141


PRSS8
31, 154


PRTN3
56, 58, 92, 180, 109, 111, 160


PRY
102


PSDA
24


PSEN1
8, 9, 39, 70, 61


PSEN2
8, 61


PSG1
70


PSMB8
64, 105, 118, 174


PSMB9
64, 105, 118, 174


PSORS1
155


PSORS2
155


PSORS3
155


PSORS4
155


PSORS5
155


PSORS6
155


PSORS7
155


PTAFR
18, 31, 50, 51, 118


PTCH 
27, 30, 31, 83, 166


PTCH2
27


PTCPRN
173


PTCRA
31


PTEN 
31, 51, 79, 167, 173, 110, 133, 154


PTGER2
42, 79


PTGER4
30, 42, 51, 79


PTGES
51


PTGIS
98, 127


PTGS1
31, 51, 133


PTH
3, 4, 31, 136, 98, 110, 132, 51, 64, 92


PTHLH
31, 110, 133


PTHR1
136


PTK2B
31, 167


PTK6
31, 51


PTMA
31, 51, 110


PTN
31, 118, 133, 141, 154, 167


PTOV1
154


PTPN1
8, 31, 64, 134, 83, 98, 132


PTPN13
154


PTPN6
31, 35, 93, 109, 112


PTPRA
31, 154


PTPRC
64, 92, 105, 123


PTPRF
31, 134


PTPRG
31, 110, 157


PTPRJ
31, 51, 56, 110


PTPRN
64, 85, 105


PTPRN2
64, 105


PTTG1
31, 51, 110, 150


PURA 
92, 109


PVR
51


PVRL1
48, 91


PXN
31, 51, 83, 167, 118, 92, 154


PYGM
31, 113, 150


RAB3A
8


RABEP1
109


RAC1
31, 51


RAD50
42, 51


RAD51
31, 154


RAD51A
31


RAD51C
31


RAD51L1
110


RAD52
31


RAD54B
93, 112


RAD54L
31, 51, 93, 112


RAG2
111


RAGE
118, 157, 176


RALA
30


RAN
154


RANBP17
109


RAP1A
110, 154


RARG
31


RASA1
27, 51, 110


RASSF1
30, 31, 110, 133, 157, 167


RB1
30, 31, 51, 110, 167, 133


RB1CC1
31


RBBP1
31


RBL2
31, 35, 79, 110, 112, 133


RBM15
109


RBM5
110, 133, 167


RBM6
110, 167


RBP1
31, 79, 107, 166


RBP1L1
31, 51, 110


RCBTB1
109


RCCP3
157


RCV1
110, 167


RDS 
113


RDX 
110, 160


REA 
31


RECK 
90


RECQL
51


REG1A
51, 141


REL
31, 92, 93, 112


RELA
8, 31, 92, 110


RELN
24, 29, 83, 162


REN
8, 64, 65, 105, 132


REST
167


RET
116, 173


RETN
64, 132, 134


RFC3
51


RFH1
98


RFP2
109


RGS4
162


RHD
86


RIL
136


RLF
110, 167


RLN1
31


RLN2
31


RNASE1
141


RNASE2
92


RNASEL
154


RNF14
154


RNF7
51, 110, 133


ROBO1
31, 110, 157


ROCK1
90


RORA 
31, 154


RPA1
31, 51, 110, 133


RPGR 
60, 113


RPL13
31, 154


RPL19
31


RPL29
51


RPL30
90


RPN1
109


RPN2
51


RPS6
110, 157


RPS6KA1
110, 133


RPS6KA3
110, 167


RPS6KB1
31


RRAD
31, 64, 132, 134


RRAS
31


RRAS2
31


RSN
93


RTN1
110


RUNX1
109, 160


RUNX2
136, 154


RXRB
162, 166


RXRG
133


RYR1
129


RYR2
169, 186


S100A1
157


S100A2
31, 118, 133


S100A6
118, 51


S100A7
31, 155


S100A9
56, 58, 155, 180


S100B
8, 61


S100P
31, 56, 154, 180


SAA1
9, 160


SAFB 
31


SAH
98, 134


SARDH
90


SAT
31, 118, 133, 154, 167, 180


SC5DL
134


SCA2
123


SCA7
113


SCABD
60


SCARB1
3


SCD
31, 51, 83


SCG2
8, 36, 160


SCG3
154


SCGB1A1
18, 154


SCGB1D2
31, 154


SCGB2A2
31


SCGB3A1
31


SCGB3A2
18


SCN10A
123


SCN1A
82


SCN1B
82


SCN4A
154


SCN5A
34, 185


SCO2
100, 129


SCP2
3


SCT
24


SCTR
140


SCYE1
118


SCZD1
162


SCZD10
162


SCZD11
162


SCZD2
162


SCZD3
162


SCZD4
162


SCZD5
162


SCZD6
162


SCZD7
162


SCZD8
162


SCZD9
162


SDC1
31, 42, 51, 122, 90, 110, 112


SDC2
24


SDHD
36, 60, 106


SE20-4
111, 112


SEL1L
31


SELE
4, 31, 51, 132, 133, 105, 110, 123, 64, 85, 92


SELL
4, 64, 92, 132, 105, 109, 123


SELP
31, 64, 92, 95, 105, 132


SELPLG
103, 109


SEMA3B
110, 133, 167


SEMA3C
110, 160


SEMA3F
110


SEPP1
51, 154


SERPINA1
47, 58, 90, 107, 110


SERPINA3
8, 31, 110


SERPINA5
172 


SERPINA7
90, 92


SERPINB3
155


SERPINB5
31, 112, 154


SERPINE1
31, 110, 154


SERPINE2
8, 102


SERPINF1
10, 31, 67, 113


SERPINF2
40, 47, 52, 109, 127, 154


SERPING1
8, 74, 111, 112, 141, 160


SERPINH1
147


SERPINI1
61


SERPINI2
31


SET
109


SFN
31, 90


SFRP1
31, 51, 180


SFTPA1
110, 159


SFTPA2
137, 159


SFTPB
110


SFTPC
110


SFTPD
104, 159, 178


SFXN5
144


SGCD 
100, 129


SH2D1A
16, 75, 88, 160, 101, 109, 112


SHBG
31, 64, 92, 134, 154, 98, 105, 132


SHC1
8, 31, 64, 132


SHFM1D
60


SHH 
27, 49, 110, 166


SHOX 
179


SI
26, 56, 74, 83


SIAH1
31, 51, 90, 154


SIAT6
31, 51


SIAT8A
118


SIAT8B
110, 133


SIAT9
30, 118, 176


SIL
109


SILV
118


SIM1
134


SIM2
70


SKP2
31, 51, 90, 109, 110, 112


SLC11A1
56, 178, 180


SLC16A1
51


SLC18A2
144, 162


SLC18A3
8


SLC19A1
31, 109


SLC19A2
64, 117


SLC1A1
10, 29, 82, 162


SLC1A2
8, 10, 82, 162


SLC1A3
8, 82


SLC22A1L
31, 110


SLC22A4
160


SLC25A1
162


SLC25A13
88


SLC26A3
51


SLC26A4
60, 173


SLC2A1
8, 31, 51, 133, 105, 110, 132, 64, 65, 92


SLC2A10
64, 132


SLC2A2
64, 105, 110, 132, 134


SLC2A3
8, 31, 92, 110, 133


SLC2A4
31, 64, 85, 134, 105, 106, 132


SLC2A5
31


SLC3A2
51


SLC4A1
8, 86, 114, 158


SLC4A4
158


SLC5A5
31


SLC5A7
8


SLC6A1
162


SLC6A14
134


SLC6A2
12, 23, 29, 62, 162


SLC6A3
23, 29, 144, 162


SLC6A4
8, 13, 23, 162, 120, 144, 153, 62, 70, 98, 24, 29, 53


SLC7A5
51


SLC9A1
65, 98, 109


SLEB1
111


SLEB3
111


SLEB4
111


SLEH1
86, 111


SLEN1
111


SLEN2
111


SLEN3
111


SLEV1
111


SLPI 
18, 58, 76, 177, 92, 110, 133


SMAP1
16


SMARCA3
51, 83


SMARCA4
31, 110, 154


SMARCB1
157


SMN1
10


SMN2
10


SMO
27, 166


SMS
31, 109


SNAI1
31, 118


SNAP25
8, 23, 29, 62, 162


SNCA 
8, 61, 70, 144


SNCAIP
144


SNCB 
8, 31, 144


SNCG 
8, 10, 31, 144


SNRPB
111, 118


SNRPN
111


SOAT1
134


SOCS3
56, 109, 112, 160


SOD1
8, 10, 31, 132, 51, 64, 105


SOD2
8, 10, 31, 110, 144, 51, 64, 105


SOD3
10


SORD 
37


SOX13
64, 105


SOX4
31


SP1
31, 110


SP100
47, 91


SP3
123


SPA17
122 


SPARC
31, 51, 69, 157, 83, 118, 154


SPARCL1
133


SPDEF
31, 154


SPG7
31, 51, 90


SPINK1
141


SPINK5
18, 20


SPINT1
31, 51, 90


SPINT2
110


SPN
8, 51, 92, 110


SPRR1B
110


SPRR3
83


SQSTM1
31, 139


SRA1
31


SRC
25, 31, 51, 109, 112, 180


SRD5A2
31, 154


SREBF1
64, 92, 132, 134


SREBF2
51, 95, 134, 154


SRF
31


SRI
112


SRP19
152


SRPX 
51, 110


SRY 
179


SS18
154, 157


SSA1
111, 133, 160


SSA2
111


SSB 
111


SST 
8, 64, 105, 132


SSTR1
31


SSTR4
154 


SSTR5
29, 31, 51, 150, 154


SSX2
30, 31, 51, 157, 112, 118, 154, 79, 90, 110


ST14
31, 51


ST7
24, 31, 51, 83, 90


ST8
138


STARD3
31, 83


STAT1
31, 51, 92, 123, 125, 94, 109, 112


STAT2
31, 109, 118


STAT5A
92


STAT5B
92, 109


STAT6
18, 31, 160


STC1
31


STE
31


STK11
118, 140


STMN1
8, 31, 110


STRC 
60


STS
31


SUCLA2
164


SULT1A1
31


SULT2A1
57


SULT2B1
31


SUSP1
112


SYBL1
29


SYCP1
31, 110, 112, 157


SYK
31, 109


SYN1
8, 162


SYN2
8, 162


SYN3
162


SYP
8, 10, 29, 61, 144, 162


TAC1
8, 31, 64, 92, 110, 167


TACC1
31


TACC3
122


TACR1
18, 56, 92, 160, 103, 120, 141


TACR2
56, 103, 160, 180


TAGLN
31


TAL1
109, 112


TAL2
109


TALDO1
123


TAM
70


TAP1
31, 64, 105, 167, 174, 110, 123, 133


TAT
47, 88, 90


TAZ
99, 129


TBX2
31


TBX22
49


TBXA2R
18, 110, 133


TBXAS1
98


TCAP 
129


TCF1
64, 90, 105, 132, 157


TCF2
26, 64, 107, 132


TCF4
29, 162


TCF7
51, 64, 105, 112


TCL1A
4, 109, 112


TCL1B
112


TCL4
112


TCL6
109


TCO
173


TCP1
70


TCPT
171


TCRA
112


TCTA
109, 167


TDGF1
31, 42, 51, 133, 141


TECTA
60


TEK
4, 31, 90, 166, 110, 118, 133


TERC
16


TERF1
31, 109


TERT
31, 51, 110, 133


TF
8, 110, 123, 167


TFAM 
88, 129


TFAP2A
51, 118, 154, 166


TFAP2C
31, 79


TFCP2
8, 92 


TFE3
157


TFF2
26, 31, 145


TFF3
51


TFG
112 


TFPI
64, 105


TFRC
8, 31, 51, 110, 123, 133, 64, 92, 105


TG
64, 92, 105, 123


TGFB2
8, 31, 51, 110, 114, 123


TGFB3
31, 51, 110


TGFBI
83


TGFBR2
30, 31, 42, 176, 151, 154, 167, 90, 110, 133, 51, 79, 83


TGFBR3
31


TGIF
83


TGM1
8, 133


TGM2
8, 31, 110, 133


TGM3
83


TGM4
154


TH
23, 24, 29, 134, 144, 162


THBD
31, 47, 51, 127, 132, 167, 110, 118, 123, 64, 92, 105


THBS2
31, 42, 51, 133, 83, 110, 127


THBS4
127


THC2
171


THPO 
31, 110


THRA 
150, 157


THRB 
31, 133, 150, 154, 157, 167


THRSP
31


THY1
109, 160


TIA1
51, 92, 109


TIAM1
31, 70, 157


TIE
4, 31, 109, 118, 157, 166


TIEG 
31, 154


TIF1
173


TIF1G
173


TIMM8A
60


TIMP2
31, 51, 110, 118


TIMP4
31


TIP47
42


TITF1
36, 110, 167


TJP1
31, 74, 77, 92, 140, 155


TJP2
31, 51, 154


TK1
31, 51


TK2
129


TKT
8


TLX1
109


TLX3
109


TM4SF2
109


TMC1
60


TMEFF2
30, 51, 154


TMIE
60


TMPRSS2
154


TMPRSS3
60


TMSB10
31, 51, 83, 154, 157


TNC
31, 51, 79, 154, 180, 98, 110, 118


TNDM
64


TNF
31, 35, 42, 133, 167, 110, 112, 114, 51, 79, 109


TNFRSF10A
31, 51, 110, 112


TNFRSF10C
51, 83, 110


TNFRSF10D
110


TNFRSF11A
139


TNFRSF11B
139


TNFRSF1B
31, 51, 64, 123, 134, 98, 105, 110, 92, 95, 97


TNFRSF5
8, 31, 35, 123, 133, 180, 92, 110, 112, 42, 56, 75


TNFRSF7
75, 92, 109, 123, 157, 111, 112, 118


TNFRSF8
92, 123


TNFRSF9
110, 160


TNFSF10
31, 51, 92, 133, 110, 122, 123


TNFSF11
31, 109, 112, 122, 154, 156


TNFSF12
111


TNFSF6
8, 26, 30, 123, 133, 92, 110, 111, 31, 51, 83


TNFSF7
92, 109, 112, 122


TNNC1
129


TNNI3
129


TNNT1
129


TNNT2
129


TNRC11
162


TOC
83


TOP1
31, 51, 109, 110, 133


TOP2B
110, 167


TP53
3, 4, 8, 167, 173, 123, 133, 140, 92, 110, 112, 31, 



51, 90


TP73
31, 35, 51, 110, 112, 118, 59, 90, 109


TP73L
26, 27, 30, 110, 83, 48, 166, 42, 51


TPD52
31


TPH1
29, 62, 162


TPI1
86


TPK1
117


TPM1
100, 129, 154


TPM2
31, 110, 129


TPM3
112, 129


TPO
60, 61, 102, 174


TPT1
8, 18, 51, 70


TPX2
110


TRA1
8, 21, 51, 88, 90


TRAF1
75, 93, 109, 112


TRAF4
31


TRAPPC1
118


TRBV5-3
92


TRC8
157


TRDD3
109, 123


TRDV3
38, 92, 109, 157


TREM2
61


TRGV9
92, 114, 160, 166


TRHR 
8, 150, 162


TRIP11
109


TRPM1
118


TRPV6
154


TSC1
30, 82, 110, 157


TSG101
31, 42, 79, 154, 90, 92, 109


TSG11
110


TSLP
20


TSN
109


TSP50
31


TSPY
154


TSPYQ1
102


TTC3
70


TTC4
31, 118


TTN
100, 124, 129


TTR
8, 9, 64, 105


TU3A
157


TUB
134


TUBB2
154


TULP1
79


TXN
31, 90, 92, 109, 133, 160


TXNRD3
90


TYMS 
31, 51, 59, 133, 109, 110, 112


TYRO3
122 


TYROBP
61


TYRP1
118


UAN
131


UBB
8, 70


UBC
157


UBE1L
110


UBE2B
102 


UBE2I
110


UBE3A
24


UBM2
118


UBTF
90, 111, 160


UCHL1
36, 51, 110, 133, 144, 167


UCN 
64, 134, 150


UCP1
134


UCP2
64, 132, 134


UCP3
64, 106, 132, 134


UFD1L
162 


UGCG
92


UGT1A1
28, 31


UGT2B15
154


UMOD
122, 157


UMPK
51


UPK1A
74


UPK1B
30, 176


UPK2
30, 176


UPK3A
30, 139, 176


UPP1
31, 51


USF1
31


USF2
31


USH1C
60


USH3A
60


USP4
110, 167


USP9Y
102


UVM1
118


VCAM1
4, 31, 51, 112, 123, 132, 64, 92, 105


VCL
31, 51


VCY2
102


VDR 
4, 31, 51, 154, 123, 132, 136, 64, 105, 109


VEGFC
31, 42, 83, 157, 110, 133, 154


VHL
157


VIL1
45


VIL2
79, 160


VIM
8, 31, 51, 110, 167


VIP
4, 8, 51, 110, 167, 133


VIPR1
92, 133, 154, 167


VIPR2
154


VLDLR
8, 31, 61


VMD2
113


VSNL1
8, 162


VSPA
179


VTN
8, 51 


VWF
31, 53, 64, 132, 92, 103, 105


WAS
171


WDM 
129


WEE1
47, 92


WFS1
29, 64, 105


WHN
6 


WHSC1
9, 122


WHSC1L1
31, 109


WHSC2
92


WISP1
31, 51


WISP2
31, 51


WISP3
31, 51


WIT-1
109


WNT1
27, 31


WNT10B
31


WNT2
24, 31, 51, 69, 83


WNT3
31, 110


WNT3A
122 


WNT7A
79, 110


WNT7B
30, 31, 83, 110


WNT8B
82


WRB
70


WRN
127


WSN
144


WT1
31, 110, 133


WTS 
134


WWOX 
31, 83, 122


XBP1
29


XCL1
56, 92


XK
29


XLKD1
31, 47


XPA
51, 110


XPC
24, 166


XRCC1
27, 31, 51, 83, 110, 166


XRCC2
31


XRCC3
30, 31, 118


XRCC5
31, 42, 51, 109, 122


YES1
51, 83, 118


YWHAG
118


YWHAH
162


YY1
92, 109


ZAP70
92, 118


ZFY
154


ZIC2
110, 167


ZNF145
109


ZNF147
31


ZNF151
51


ZNF198
112


ZNF217
31, 51, 154


ZNFN1A1
109, 112


ZNFN1A2
109


ZXDA
179


ZXDB
179

## Claims

1. A nucleic acid selected from the group consisting of:
(a) a nucleic acid consisting of the nucleotide sequence set forth in SEQ ID NO: 4;
(b) a RNA encoded by the nucleic acid of (a), wherein the RNA is identical in length to (a);
(c) a nucleic acid at least 90% identical to (a) or (b); and
(d) the complement of one of the nucleic acids of (a)-(c), wherein the complement is identical in length to the one of the nucleic acids of (a)-(c);

wherein the nucleic acid contains a non-naturally occurring nucleotide or ribonucleotide.

2. A probe comprising a heterologous nucleic acid, wherein the heterologous nucleic acid consists of a nucleic acid sequence selected from the group consisting of:
(a) the sequence set forth in SEQ ID NO: 4;
(b) a RNA sequence encoded by the sequence of (a), wherein the RNA sequence is identical in length to (a);
(c) a sequence at least 90% identical to (a) or (b); and
(d) the complement of one of the sequences of (a)-(c), wherein the complement is identical in length to the one of the sequences of (a)-(c),

wherein the probe comprises at least one of a non-naturally occurring nucleotide or ribonucleotide, a label, and a solid substrate.

3. A vector comprising a heterologous nucleic acid, wherein the heterologous nucleic acid consists of a nucleic acid sequence selected from the group consisting of:
(a) the sequence set forth in SEQ ID NO: 4;
(b) a RNA sequence encoded by the sequence of (a), wherein the RNA sequence is identical in length to (a);
(c) a sequence at least 90% identical to (a) or (b); and
(d) the complement of one of the sequences of (a)-(c), wherein the complement is identical in length to the one of the sequences of (a)-(c).