Abstract:
The present application relates to gene analysis and, in particular, to gene expression profiling for identifying molecular signature of cancer disease, in particular the G1 phase of the cell cycle, such as myeloproliferative disorders (MPD) or breast cancer and studying cancer. 
     More particularly, the application is directed to a method for analyzing differential gene expression associated with cancer disease, in particular the G1 phase of the cell cycle, such as myeloproliferative disorders (MPD) or breast cancer comprising detection of upregulation and/or downregulation of a pool of polynucleotide sequences in a cell or tissue sample, said pool corresponding to all or part the polynucleotide sequences, subsequences or complements thereof, of the genes listed in Tables 1, 2 and 3.

Description:
PRIORITY 
       [0001]    This Application claims priority to U.S. Provisional Application No. 60/874,357 filed on 12 Dec. 2006; the entire contents of which are hereby incorporated herein by reference. 
     
    
     TECHNICAL FIELD 
       [0002]    This disclosure relates to gene analysis and, in particular, to gene expression profiling for identifying molecular signature of cancer disease, in particular the G1 phase of the cell cycle, such as myeloproliferative disorders (MPD) or breast cancer and studying cancer. 
       BACKGROUND 
       [0003]    Myeloproliferative disorders (MPD) are clonal proliferative diseases of the hematopoietic stem cells. After an initial phase they may progress to an acute syndrome. V617F mutation of the JAK2 kinase are found in polycythemia vera, essential thrombocythemia, and idiopathic myelofibrosis. BCR-ABL fusion occurs in chronic myeloid leukemia, and a variety of fusions involving PDGF and FGF receptors are found in other MPDs. Fusion kinases that result from a translocation are made of a constitutively activated kinase domain and an N-terminal region encoded by a partner gene. The activated kinase triggers sustained proliferation and survival of the hematopoietic cells but maturation is not affected. 
         [0004]    Because of the side effects and risk of cancer therapy as well as resistance of certain patient to the treatment with certain drug, it would be desirable to offer new means to monitor cancer treatment and to be able to identify patients in need of such treatment. 
       SUMMARY 
       [0005]    We provide methods for analyzing differential gene expression associated with cancer disease, more particularly, the G1 phase of the cell cycle such as myeloproliferative disorders (MPD) or breast cancer, comprising detecting the upregulation and/or downregulation of a pool of polynucleotide sequences in a cell or tissue sample, the pool corresponding to all or part the polynucleotide sequences, subsequences or complement thereof, of the genes listed in Tables 1, 2 and 3. 
         [0006]    More particularly, the methods are carried out on a tumor cell or tissue sample. It may be any sample that may be taken from a patient, such as for example serum, plasma, urine or a biopsy sample. 
         [0007]    Upregulation and/or downregulation of a pool of polynucleotide sequences according to the method of the present invention identify a molecular signature of activated MPD kinase. 
         [0008]    Table 2 displays 188 upregulated genes/EST and table 3 displays 48 genes/EST downregulated in activated kinase-expressing cells. 
         [0009]    Table 1 represents the most significant (p-value inferior at 2·10 −2 ) and most often represented (including at least 3 genes) biological processes. Many of the upregulated genes encode nucleolar proteins involved in “ribosome biogenesis” (GO:0007046, 6 genes, p=4.28·10 −11 ), “rRNA processing” (GO:0006364; 7 genes, p=3.07·10 −11 ), and “protein biosynthesis” (GO:0006412, 9 genes, p=3.60·10 −0.5 ). 
         [0010]    Tables 1, 2 and 3 indicate the name of the gene (gene Symbol). We define the nucleotide sequences by the name of the gene or fragments thereof. Each polynucleotide sequence in Tables 2 and 3 may be considered as a marker of the corresponding gene. Each marker corresponds to a gene in the human genome, i.e., such marker is identifiable as all or a portion of a gene. Any RNA transcribed from a marker gene (mRNAs), any cDNA or cRNA produced therefrom, and any nucleic acid derived therefrom, such as synthetic nucleic acid having a sequence derived from the gene corresponding to the marker gene are also encompassed by the present invention. 
         [0011]    A “pool of polynucleotide sequences” may comprise one or more sequences, preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 350, 400, 450, 500 sequences. 
         [0012]    The number of genes may vary in the range of from 1 to the total number of genes described in Tables 1, 2 or 3, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130, 140, 150, 160, 170, 180, 188 genes, depending of the number of genes in said tables. 
         [0013]    The pool of polynucleotide sequences may comprise the polynucleotide sequences, subsequences or complement thereof, of the genes listed in Tables 2. More particularly, the methods relate to upregulated genes encoding nucleolar proteins (CIRH1A, LARP1, NOL1, NOL11, NOL5, NOL5A, NOLA1, NOLA2, NOLC1, MKI67IP, SFRS2, SURF6), ribosomal proteins (RPL3, RPL12, RPL41, RPS9, RRS1), small nuclear ribonucleoproteins and interactors (U3/MPHOSPH10, LSM2, RNU22, RNU3IP2), components of RNA polymerase I (POLR1A, POLR1B), II (POLR2H, TAF9) and III (POLR3E, POLR3H), DEAD-box (DDX18, DDX56) and WD repeat (WDR4, WDR43, WDR74, WDR77, GRWD1, PWP1) proteins, eukaryotic initiation and elongation factors (EIF1A, EIF3S1, EIF3S4, EEF1E1), and components of the exosome (EXOSC1, EXOSC2, EXOSC6). 
         [0014]    The genes also relate to upregulated genes encoding proteins of the NOL5A-associated preribosomal ribonucleoprotein complex involved in pre-rRNA processing: NOL5A, PPAN, NOLC1, and BXDC2. The gene encoding EBNA1BP2 was upregulated; it encodes a protein that binds to nucleolar FGF3 and is regularly upregulated in tumors. 
         [0015]    The genes further relate to the most upregulated sequence GAS5, a non-protein-coding multiple small nucleolar RNA (snoRNA). 
         [0016]    Other significant processed genes includes “protein folding” (4 genes), “ubiquitin-dependent protein catabolism” (3 genes), “nuclear mRNA splicing, via spliceosome” (3 genes), and “regulation of cell cycle” (3 genes). 
         [0017]    A second major category of upregulated genes encode CCND2 (cyclin D2) and CDC25A, two major regulators needed for G1 progression. 
         [0018]    Moreover, the list of upregulated genes included MYC. Many genes upregulated by MYC and NMYC oncogenes were also upregulated in our experiments, including CCND2, CDC25A and others (DDX18, EBNA1BP2, EEF1E1, MAT2A, MKI67IP, NOL5A, NOLA1, PHB, SFRS2, SHMT1, SLC16A1, SURF6, SRM, RPL3, RPL12, RPL41, RPS9 and RRS1). 
         [0019]    The pool of polynucleotide sequences may include all or part the polynucleotide sequences, subsequences or complement thereof, of the genes listed in Tables 3. More particularly, the pool relates to downregulated genes encoding proteins with known or potential inhibitory function such as PIAS3, an inhibitor of STAT3, one of the main substrates of MPD kinases, and regulator of CDC25A, Erbin, and PLZF/ZBTB16, a MYC repressor. 
         [0020]    The detection of over or under expression of polynucleotide sequences may be carried out by FISH or IHC. The detection may be performed on DNA microarrays. The level of the RNA transcripts can be measured by any available technique such as quantitative PCR. 
         [0021]    We further provide a polynucleotide library useful for the molecular characterization of a cancer comprising or corresponding to a pool of polynucleotide sequences either upregulated or downregulated in tissue, said pool corresponding to all or part of the polynucleotide sequences selected as defined above. 
         [0022]    The polynucleotide library may be immobilized on a solid support, for example selected from the group comprising nylon membrane, nitrocellulose membrane, glass slide, glass beads, membranes on glass support or silicon chip, plastic support. 
         [0023]    We further provides a method for analysing differential gene expression associated with cancer disease, comprising:
       a) obtaining a polynucleotide sample from a patient, and   b) reacting the polynucleotide sample obtained in step (a) with a polynucleotide library as defined above, and   c) detecting the reaction product of step (b).       
 
         [0027]    The polynucleotide sample may be labelled before reaction step (b). The label may be selected from the group consisting of at least one of radioactive, calorimetric, enzymatic, molecular amplification, bioluminescent or fluorescent labels. Preferably, the label is calorimetric, e.g., biotin or digoxygenin. 
         [0028]    The method may further comprise:
       a) obtaining a control polynucleotide sample,   b) reacting said control sample with the polynucleotide library, for example by hybridising the polynucleotide sample with the polynucleotide library,   c) detecting a control sample reaction product, and   d) comparing the amount of the polynucleotide sample reaction product to the amount of the control sample reaction product.       
 
         [0033]    The polynucleotide sample may be cDNA, RNA or mRNA. The mRNA may be isolated from the polynucleotide sample and cDNA may be obtained by reverse transcription of said mRNA. 
         [0034]    We further provide a method for determining the nature of a cancer from a cancer cell or tissue comprising the implementation of the method on nucleic acids from cells or tissues from a patient. 
         [0035]    More particularly, the method is useful for profiling samples of various human MPDs. It may help define the initial steps of oncogenesis, for which G1 activation may be important. Cell quiescence may be defined by the absence of protein synthesis, whereas proliferation starts with nucleolar activity, ribosome biogenesis and rRNA processing. Second, MPDs can benefit from treatment targeting not only the activated kinases but also the PI3K/AKT/TOR signaling pathway and the G1 phase of the cell cycle, in synergy with anti-kinase drugs and/or in case of resistance. G1 targeting is frequent in many types of cancer. The signature can be used in transcriptome studies of any type of cancer to identify G1 activation, classify tumors, and use the appropriate drugs. 
         [0036]    Therefore, we further provide a method of prognosis or diagnostic or prediction of tumours susceptible to a molecule acting on the G1 phase of the cell cycle such as rapamycine and its derivatives, and therefore we provide a method for monitoring the treatment of a patient with a cancer comprising the implementation of the method of analysis disclosed hereabove on nucleic acids from a patient to identify the corresponding signature. 
         [0037]    We also provide a method of selection of patient susceptible to be treated with molecule acting on the G1 phase of the cell cycle such as rapamycine or its derivative, comprising the implementation of the method hereabove on nucleic acids from a patient in order to identify the corresponding signature. 
         [0038]    This signature provides tools for classifying basal tumors for which the high proliferation results from the PI3K/TOR pathway. Therefore, we provide methods for determining whether a tumor has an activated proliferation according to PI3K/TOR and is sensitive to chemotherapy. 
     
    
     
       BRIEF DESCRIPTION OF THE DRAWING 
         [0039]      FIG. 1  shows gene expression profiling of Ba/F3 cell samples identifies a molecular signature of activated MPD kinases. A. Hierarchical clustering of 15 samples using the 294 genes identified as discriminator between Ba/F3 cells transfected by activated kinases (9 samples: BCR-ABL, 2 BCR-FGFR1, 2 CEP1-FGFR1, 2 FOP-FGFR1 and 2 V617F JAK2) to that of parental Ba/F3 cells (4 samples) and Ba/F3 expressing a kinase defective mutant of FOP-FGFR1 (2 samples). Each row represents a gene, each column a sample. The log 2 -transformed expression level of each gene in a single sample is relative to its median abundance across all samples and is depicted according to the colour scale shown at the bottom. Red and green indicate expression levels respectively above and below the median. The magnitude of deviation from the median is represented by the color saturation. The dendrogram of samples (above matrix) represents overall similarities in gene expression profiles and is zoomed in B. Branches of the dendrograms are color-coded as follows: red for fusion kinase-expressing Ba/F3 cells and green for control cells. Some genes included in the signature (framed in red for the upregulated genes and in green for the down-regulated genes) are noted to the right of the data matrix and referenced by their abbreviation as used in EntrezGene. A discriminating score (DS) was calculated for each gene. DS=(M1−M2)/(S1+S2) where M1 and S1 respectively represent mean and SD of expression levels of the gene in subgroup 1, and M2 and S2 in subgroup 2. Confidence levels were estimated by 100 random permutations of samples. A “leave-one-out” procedure estimated the accuracy of prediction of the signatures and the validity of our supervised analysis. B. Top, dendrogram of samples. Down, correlation between the molecular grouping based on the combined expression of the 294 genes and the status of samples. C. Western blot analysis of cyclin D2 in Ba/F3 expressing activated MPD kinases. NP40-extracted proteins were separated by gel electrophoresis (SDS-PAGE), transferred onto membrane (Hybond-C Extra, GE Healthcare UK, Buckinghamshire, UK), and probed with rabbit polyclonal anti-cyclin D2 (M-20, Santa Cruz Biotechnology, Santa Cruz, Calif.). Cyclin D2 (top) is upregulated in Ba/F3 cells expressing MPD kinases compared to control Ba/F3 cells (untransfected, FOP-FGFR1 KD, MIGR and JAK2 WT). Total cell lysates were probed with mouse monoclonal anti-α-tubulin (B-5-1-2, Sigma-Aldrich, Saint-Quentin Fallavier, France) to compare the amount of protein in the lysates (bottom). 
           [0040]      FIG. 2  provides the murine polynucleotide sequences from Ba/F3 cell line of the genes/EST listed in tables 1, 2 and 3 where the genes/EST are identified by their names and access numbers (Prob set). 
       
    
    
     DETAILED DESCRIPTION 
       [0041]    Myeloproliferative disorders (MPD) are clonal hematopoietic diseases characterized by the proliferation and expansion of one or several myeloid cell lineages in the bone marrow. During the chronic phase, the cells follow their normal differentiation pathway and become mature blood cells. During a second phase, an acute syndrome may occur. The conventional classification separates MPDs in clinical entities. These include chronic myeloid leukemia (CML), chronic neutrophilic leukemia, chronic eosinophilic leukemia, polycythemia vera (PV), essential thrombocythemia (ET) and idiopathic myelofibrosis (IMF). MPDs with different syndromes and molecular abnormalities are grouped in non-classical MPDs. Systemic mastocytosis is not classically included in MPDs but is a related disease. 
         [0042]    We studied the gene expression profiles of murine Ba/F3 cells transfected by various oncogenic MPD kinases by using whole-genome Affymetrix 430 2.0 mouse oligonucleotide microarrays (www.Affymetrix.com). Ba/F3 cells were grown in RPMI medium supplemented with 10% fetal calf serum (FCS) and IL3. Expression of an MPD kinase bypasses the IL3 dependence of Ba/F3 cells. RNA was extracted by using Trizol (Trizol Reagent, Invitrogen Life Technologies, Carlsbad, Calif.) from frozen pellets of: i)—Ba/F3 cells, ii)—Ba/F3 transfected with different pCDNA expression vectors expressing a mutant, kinase-defective FOP-FGFR1 KD or an oncogenic MPD kinase (BCR-ABL, FOP-FGFR1, CEP1-FGFR1, BCR-FGFR1), and iii)—Ba/F3 transfected by the MIGR vector, either empty (MIGR) or with JAK2 (JAK2 WT, mutated V617F JAK2 or mutated V617F IND JAK2 i.e. able to grow independently of IL3). Before RNA extraction, cells were starved for 7 hours in RPMI plus 0.5% FCS. RNA integrity was controlled by microanalysis (Agilent Bioanalyzer, Palo Alto, Calif.). Preparation of cRNA, hybridizations, washes, detection and quantification were done as recommended by the supplier (Affymetrix). Data were analyzed by the RMA (Robust Multichip Average) method in R using Bioconductor and associated package. Before analysis, a filtering process removed from the dataset the genes with low and poorly measured expression as defined by an expression value inferior to 100 units in all samples, retaining 17.885 genes/ESTs. For paired samples, RNA was prepared independently from different cultures of cells. The correlation between paired samples ranged between 0.97 and 0.98. 
         [0043]    Gene expression profiles of Ba/F3 cells transfected by fusion or mutated kinases (9 samples: BCR-ABL, 2 BCR-FGFR1, 2 CEP1-FGFR1, 2 FOP-FGFR1, 2 V617F JAK2) were compared to that of control cells (6 samples) including parental Ba/F3 cells (4 samples) and Ba/F3 expressing a kinase-defective mutant of FOP-FGFR1 (2 samples). Supervised analysis, based on 17,885 filtered probe-sets, identified 294 differentially expressed probe sets (theoretical number of produced false positives=1.7) ( FIGS. 1A , B), representing 228 genes and 8 ESTs, of which 188 were upregulated and 48 downregulated in activated kinase-expressing cells (Tables 2 and 3). 
         [0044]    To translate the RNA expression profiles into functionality, discriminator genes/ESTs were interrogated by Onto-Express. 7  Table 1 represents the most significant (p-value inferior at 3·10 −2 ) and most often represented (including at least 3 genes) biological processes. Many of the upregulated genes encode nucleolar proteins involved in “ribosome biogenesis” (GO:0007046, 6 genes, p=4.28·10 −11 ), “rRNA processing” (GO:0006364; 7 genes, p=3.07·10 −11 ), and “protein biosynthesis” (GO:0006412, 9 genes, p=3.60·10 −05 ). Upregulated genes encode nucleolar proteins (CIRH1A, LARP1, NOL1, NOL11, NOL5, NOL5A, NOLA1, NOLA2, NOLC1, MKI67IP, SFRS2, SURF6), ribosomal proteins (RPL3, RPL12, RPL41, RPS9, RRS1), small nuclear ribonucleoproteins and interactors (U3/MPHOSPH10, LSM2, RNU22, RNU3IP2), components of RNA polymerase I (POLR1A, POLR1B), II (POLR2H, TAF9) and III (POLR3E, POLR3H), DEAD-box (DDX18, DDX56) and WD repeat (WDR4, WDR43, WDR74, WDR77, GRWD1, PWP1) proteins, eukaryotic initiation and elongation factors (EIF1A, EIF3S1, EIF3S4, EEF1E1), and components of the exosome (EXOSC1, EXOSC2, EXOSC6). Upregulated genes also encode proteins of the NOL5A-associated preribosomal ribonucleoprotein complex involved in pre-rRNA processing: NOL5A, PPAN, NOLC1, and BXDC2. The gene encoding EBNA1BP2 was upregulated; it encodes a protein that binds to nucleolar FGF3 and is regularly upregulated in tumors. The most upregulated sequence was GAS5, a non-protein-coding multiple small nucleolar RNA (snoRNA). 
         [0045]    Other significant processes included “protein folding” (GO:0006457; 4 genes, p=6.72·10 −03 ), “ubiquitin-dependent protein catabolism” (GO:0006511, 3 genes, p=1.47·10 −02 ), “nuclear mRNA splicing, via spliceosome” (GO:0000398, 3 genes, p=1.65·10 −02 ), and “regulation of cell cycle” (GO:0000074, 3 genes, p=1.65·10 −02 ). The second major category of upregulated genes encode CCND2 (cyclin D2) and CDC25A, two major regulators needed for G1 progression. CCND2 RNA was found upregulated by BCR-ABL in previous gene expression studies. Cyclin D2 is necessary for BCR-ABL-induced activity. Inhibition of V617F JAK2 correlates with decreased expression of cyclin D2. Other G1 cyclins may play a role in the oncogenic activity of fusion kinases but cyclin D2 seems to be a rate-limiting element. We used Western blot analysis to validate the differential expression of cyclin D2. The amount of cyclin D2 protein was increased in Ba/F3 cells expressing activated kinases as compared to controls ( FIG. 1C ), in agreement with mRNA expression results. 
         [0046]    MYC directly or indirectly regulates the G1 phase of the cell cycle. The list of upregulated genes included MYC. Many genes upregulated by MYC and NMYC oncogenes were also upregulated in our experiments, including CCND2, CDC25A and others (DDX18, EBNA1BP2, EEF1E1, MAT2A, MKI67IP, NOL5A, NOLA1, PHB, SFRS2, SHMT1, SLC16A1, SURF6, SRM, RPL3, RPL12, RPL41, RPS9 and RRS1). This similarity suggests that MYC proteins and MPD kinases have similar oncogenic effects, whose main target would be the CDKN2-RB protein pathway during the G1 phase of the cell cycle. Once induced, MYC may in turn act on the transcription of G1/S regulators and genes involved in protein synthesis. MPD fusion kinases are thought to target the hematopoietic stem cell. Activation of MYC is in perfect agreement with what we know of stem cell proliferation. A similar program was also turned on by IL3 stimulation (not shown). 
         [0047]    Downregulated genes were more difficult to classify with Onto-Express, but several encode proteins with known or potential inhibitory function such as PIAS3, an inhibitor of STAT3, one of the main substrates of MPD kinases, and regulator of CDC25A, Erbin, and PLZF/ZBTB16, a MYC repressor. 
         [0048]    We tested the validity of our classification by the “leave-one-out” cross-validation method. Iteratively, one of the 15 samples was removed, and a multigene predictor was generated from the remaining samples: 93% of samples were correctly assigned by the predictors with a sensitivity of 89% and a specificity of 100%. 
         [0049]    Thus, in Ba/F3 cells, MPD fusion kinases induce both G1 activators and protein synthesis components, thus starting the cell proliferation machinery. This effect may be mediated by the PI3 kinase-AKT-TOR pathway, which controls and coordinates both protein synthesis and early phases of the cell cycle. Prominent downstream targets of the AKT pathway are cyclins D1, D2 and MYC. 
         [0050]    The subject matter of the references set forth below are hereby incorporated by reference in their entirety:
   1. Percy M J, McMullin M F. The V617F JAK2 mutation and the myeloproliferative disorders.  Hematol Oncol  2005; 23: 91-93.   2. Delaval B, Letard S, Lelievre H, Chevrier V, Daviet L, Dubreuil P, et al. Oncogenic tyrosine kinase of malignant hemopathy targets the centrosome.  Cancer Res  2005; 65: 7231-7240.   3. De Keersmaecker K, Cools J. Chronic myeloproliferative disorders: a tyrosine kinase tale.  Leukemia  2006; 20: 200-205.   4. Guasch G, Ollendorff V, Borg J P, Birnbaum D, Pebusque M J. 8p12 stem cell myeloproliferative disorder: the FOP-fibroblast growth factor receptor 1 fusion protein of the t(6;8) translocation induces cell survival mediated by mitogen-activated protein kinase and phosphatidylinositol 3-kinase/Akt/mTOR pathways.  Mol Cell Biol  2001; 21: 8129-8142.   5. Staerk J, Kallin A, Demoulin J B, Vainchenker W, Constantinescu S N. JAK1 and Tyk2 activation by the homologous polycythemia vera JAK2 V617F mutation: cross-talk with IGF1 receptor.  J Biol Chem  2005; 280: 41893-41899.   6. James C, Ugo V, Le Couedic J P, Staerk J, Delhommeau F, Lacout C, et al. A unique clonal JAK2 mutation leading to constitutive signalling causes polycythaemia vera.  Nature  2005; 434: 1144-1148.   7. Lamond A, Mann M. Nucleolar Proteome Database v 2.0. 2005 [cited september 06]; Available from: www.lamondlab.com/NoPDB.   8. Butler J S. The yin and yang of the exosome.  Trends Cell Biol  2002; 12: 90-96.   9. Hayano T, Yanagida M, Yamauchi Y, Shinkawa T, Isobe T, Takahashi N. Proteomic analysis of human Nop56p-associated pre-ribosomal ribonucleoprotein complexes. Possible link between Nop56p and the nucleolar protein treacle responsible for Treacher Collins syndrome.  J Biol Chem  2003; 278: 34309-34319.   10. Reimers K, Antoine M, Zapatka M, Blecken V, Dickson C, Kiefer P. NoBP, a nuclear fibroblast growth factor 3 binding protein, is cell cycle regulated and promotes cell growth.  Mol Cell Biol  2001; 21: 4996-5007.   11. Pilarsky C, Wenzig M, Specht T, Saeger H D, Grutzmann R. Identification and validation of commonly overexpressed genes in solid tumors by comparison of microarray data.  Neoplasia  2004; 6: 744-750.   12. Smith C M, Steitz J A. Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5′-terminal oligopyrimidine gene family reveals common features of snoRNA host genes.  Mol Cell Biol  1998; 18: 6897-6909.   13. Parada Y, Banerji L, Glassford J, Lea N C, Collado M, Rivas C, et al. BCR-ABL and interleukin 3 promote haematopoietic cell proliferation and survival through modulation of cyclin D2 and p27Kip1 expression.  J Biol Chem  2001; 276: 23572-23580.   14. Deininger M W, Vieira S, Mendiola R, Schultheis B, Goldman J M, Melo J V. BCR-ABL tyrosine kinase activity regulates the expression of multiple genes implicated in the pathogenesis of chronic myeloid leukemia.  Cancer Res  2000; 60: 2049-2055.   15. Jena N, Deng M, Sicinska E, Sicinski P, Daley G Q. Critical role for cyclin D2 in BCR/ABL-induced proliferation of hematopoietic cells.  Cancer Res  2002; 62: 535-541.   16. Walz C, Crowley B J, Hudon H E, Gramlich J L, Neuberg D S, Podar K, et al. Activated JAK2 with the V617F point mutation promotes G1/S-phase transition.  J Biol Chem  2006.   17. Nasi S, Ciarapica R, Jucker R, Rosati J, Soucek L. Making decisions through Myc.  FEBS Lett  2001; 490: 153-162.   18. Bouchard C, Thieke K, Maier A, Saffrich R, Hanley-Hyde J, Ansorge W, et al. Direct induction of cyclin D2 by Myc contributes to cell cycle progression and sequestration of p27.  Embo J  1999; 18: 5321-5333.   19. Perez-Roger I, Kim S H, Griffiths B, Sewing A, Land H. Cyclins D1 and D2 mediate myc-induced proliferation via sequestration of p27(Kip1) and p21(Cip1).  Embo J  1999; 18: 5310-5320.   20. Coller H A, Grandori C, Tamayo P, Colbert T, Lander E S, Eisenman R N, et al. Expression analysis with oligonucleotide microarrays reveals that MYC regulates genes involved in growth, cell cycle, signaling, and adhesion.  Proc Natl Acad Sci USA  2000; 97: 3260-3265.   21. Zeller K I, Jegga A G, Aronow B J, O&#39;Donnell K A, Dang C V. An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.  Genome Biol  2003; 4: R69.   22. Schlosser I, Holzel M, Hoffmann R, Burtscher H, Kohlhuber F, Schuhmacher M, et al. Dissection of transcriptional programmes in response to serum and c-Myc in a human B-cell line.  Oncogene  2005; 24: 520-524.   23. Boon K, Caron H N, van Asperen R, Valentijn L, Hermus M C, van Sluis P, et al. N-myc enhances the expression of a large set of genes functioning in ribosome biogenesis and protein synthesis.  Embo J  2001; 20: 1383-1393.   24. Steiner P, Rudolph B, Muller D, Eilers M. The functions of Myc in cell cycle progression and apoptosis.  Prog Cell Cycle Res  1996; 2: 73-82.   25. Moore K A, Lemischka I R. Stem cells and their niches.  Science  2006; 311: 1880-1885.   26. Barre B, Vigneron A, Coqueret O. The STAT3 transcription factor is a target for the Myc and riboblastoma proteins on the Cdc25A promoter.  J Biol Chem  2005; 280: 15673-15681.   27. McConnell M J, Chevallier N, Berkofsky-Fessler W, Giltnane J M, Malani R B, Staudt L M, et al. Growth suppression by acute promyelocytic leukemia-associated protein PLZF is mediated by repression of c-myc expression.  Mol Cell Biol  2003; 23: 9375-9388.   28. Golub T R, Slonim D K, Tamayo P, Huard C, Gaasenbeek M, Mesirov J P, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.  Science  1999; 286: 531-537.   29. Ruggero D, Sonenberg N. The Akt of translational control.  Oncogene  2005; 24: 7426-7434.   30. Gera J F, Mellinghoff I K, Shi Y, Rettig M B, Tran C, Hsu J H, et al. AKT activity determines sensitivity to mammalian target of rapamycin (mTOR) inhibitors by regulating cyclin D1 and c-myc expression.  J Biol Chem  2004; 279: 2737-2746.   31. Malumbres M, Barbacid M. To cycle or not to cycle: a critical decision in cancer.  Nat Rev Cancer  2001; 1: 222-231.   
 
         [0000]    
       
         
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 1 
               
             
             
               
                   
               
               
                 Selection of discriminant genes classified by Onto-Express 
               
             
          
           
               
                   
                   
                   
                   
                   
                 Discriminating 
               
               
                 GO ID 
                 Biological process 
                 P-value 
                 Gene Symbol 
                 Probe set 
                 Score 
               
               
                   
               
               
                 GO:0006364 
                 rRNA processing 
                 3.07E−11 
                 Nola1 
                 1418305_s_at 
                 2.10 
               
               
                   
                   
                   
                 Exosc2 
                 1426630_at 
                 1.96 
               
               
                   
                   
                   
                 Rnu3ip2 
                 1451293_at 
                 1.46 
               
               
                   
                   
                   
                 Mphosph10 
                 1429080_at 
                 1.42 
               
               
                   
                   
                   
                 Ddx56 
                 1423815_at 
                 1.41 
               
               
                   
                   
                   
                 Ebna1bp2 
                 1428315_at 
                 1.31 
               
               
                   
                   
                   
                 Exosc1 
                 1452012_a_at 
                 1.31 
               
               
                 GO:0007046 
                 ribosome biogenesis 
                 4.82E−11 
                 Rpl12 
                 1435655_at 
                 1.73 
               
               
                   
                   
                   
                 1110017C15Rik 
                 1448480_at 
                 1.63 
               
               
                   
                   
                   
                 Rrs1 
                 1456865_x_at 
                 1.63 
               
               
                   
                   
                   
                 Nol5a 
                 1426533_at 
                 1.59 
               
               
                   
                   
                   
                 Gtpbp4 
                 1450873_at 
                 1.40 
               
               
                   
                   
                   
                 2610012O22Rik 
                 1423823_at 
                 1.30 
               
               
                 GO:0006412 
                 protein biosynthesis 
                 3.60E−05 
                 Rpl41 
                 1454639_x_at 
                 1.90 
               
               
                   
                   
                   
                 Mrps18b 
                 1451164_a_at 
                 1.82 
               
               
                   
                   
                   
                 Rpl3 
                 1438527_at 
                 1.79 
               
               
                   
                   
                   
                 Rps9 
                 1426958_at 
                 1.69 
               
               
                   
                   
                   
                 Eif3s1 
                 1426394_at 
                 1.53 
               
               
                   
                   
                   
                 Nola2 
                 1416605_at 
                 1.51 
               
               
                   
                   
                   
                 Itgb4bp 
                 1427578_a_at 
                 1.47 
               
               
                   
                   
                   
                 Eef1e1 
                 1449044_at 
                 1.45 
               
               
                   
                   
                   
                 Eif3s4 
                 1417718_at 
                 1.38 
               
               
                 GO:0006457 
                 protein folding 
                 6.72E−03 
                 Dnajc11 
                 1433880_at 
                 1.38 
               
               
                   
                   
                   
                 Cct3 
                 1448178_a_at 
                 1.33 
               
               
                   
                   
                   
                 Ero1l 
                 1419030_at 
                 1.32 
               
               
                   
                   
                   
                 Hyou1 
                 1423291_s_at 
                 1.31 
               
               
                 GO:0006511 
                 ubiquitin-dependent 
                 1.47E−02 
                 Usp39 
                 1437007_x_at 
                 1.51 
               
               
                   
                 protein catabolism 
                   
                 Siah2 
                 1448171_at 
                 1.30 
               
               
                   
                   
                   
                 Usp10 
                 1448230_at 
                 1.29 
               
               
                 GO:0000398 
                 nuclear mRNA splicing, 
                 1.65E−02 
                 Mki67ip 
                 1424001_at 
                 1.88 
               
               
                   
                 via spliceosome 
                   
                 Pprc1 
                 1426381_at 
                 1.86 
               
               
                   
                   
                   
                 Sfrs2 
                 1415807_s_at 
                 1.46 
               
               
                 GO:0000074 
                 regulation of cell cycle 
                 1.65E−02 
                 Axl 
                 1423586_at 
                 1.65 
               
               
                   
                   
                   
                 Ccnd2 
                 1430127_a_at 
                 1.51 
               
               
                   
                   
                   
                 Cdc25a 
                 1417132_at 
                 1.43 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 2 
               
             
             
               
                   
               
               
                 188 upregulated genes/EST associated with their biological process ordered by discriminating score 
               
             
          
           
               
                   
                   
                   
                   
                   
                 Onto- 
               
               
                   
                   
                 Discriminating 
                   
                   
                 Express P           
               
               
                 Probe set 
                 Gene Symbol 
                 Score 
                 GO ID 
                 Onto-Express Biological Process 
                 value 
               
               
                   
               
               
                 1455904_at 
                 Gas5 
                 3.32 
                 null 
                 unknownP 
                 0.33 
               
               
                 1435998_at 
                 na 
                 3.03 
                 null 
                 unknownP 
                 0.33 
               
               
                 1416345_at 
                 Timm8a 
                 2.57 
                 GO:0006626 
                 protein-mitochondrial targeting 
                 0.00 
               
               
                 1455643_s_at 
                 AW550801 
                 2.32 
                 null 
                 unknownP 
                 0.33 
               
               
                 1429061_at 
                 1810063B05Rik 
                 2.29 
                 null 
                 unknownP 
                 0.33 
               
               
                 1425177_at 
                 Shmt1 
                 2.28 
                 GO:0006563 
                 L-serine metabolism 
                 0.00 
               
               
                 1423138_at 
                 Wdr4 
                 2.25 
                 GO:0008033 
                 tRNA processing 
                 0.02 
               
               
                 1416376_at 
                 1810014L12Rik 
                 2.21 
                 null 
                 unknownP 
                 0.33 
               
               
                 1456117_at 
                 2600005C20Rik 
                 2.14 
                 null 
                 unknownP 
                 0.33 
               
               
                 1428529_at 
                 2810026P18Rik 
                 2.12 
                 null 
                 unknownP 
                 0.33 
               
               
                 1418305_s_at 
                 Nola1 
                 2.10 
                 GO:0006364 
                 rRNA processing 
                 0.00 
               
               
                 1451509_at 
                 Taf9 
                 2.10 
                 GO:0006352 
                 transcription initiation 
                 0.00 
               
               
                 1454214_a_at 
                 2410019A14Rik 
                 2.10 
                 null 
                 unknownP 
                 0.33 
               
               
                 1425820_x_at 
                 Gpatc4 
                 2.08 
                 null 
                 unknownP 
                 0.33 
               
               
                 1433467_at 
                 Slc7a6 
                 2.03 
                 GO:0006810 
                 transport 
                 0.20 
               
               
                 1441415_at 
                 Spred2 
                 2.02 
                 GO:0000188 
                 inactivation of MAPK 
                 0.00 
               
               
                 1426630_at 
                 Exosc2 
                 1.96 
                 GO:0006364 
                 rRNA processing 
                 0.00 
               
               
                 1437592_x_at 
                 1700023O11Rik 
                 1.93 
                 null 
                 unknownP 
                 0.33 
               
               
                 1424620_at 
                 D13Wsu177e 
                 1.92 
                 null 
                 unknownP 
                 0.33 
               
               
                 1455832_a_at 
                 Umps 
                 1.91 
                 GO:0006221 
                 pyrimidine nucleotide biosynthesis 
                 0.00 
               
               
                 1421260_a_at 
                 Srm 
                 1.91 
                 GO:0008295 
                 spermidine biosynthesis 
                 0.00 
               
               
                 1428869_at 
                 Nolc1 
                 1.90 
                 GO:0007000 
                 nucleolus organization and biogenesis 
                 0.00 
               
               
                 1454639_x_at 
                 Rpl41 
                 1.90 
                 GO:0006412 
                 protein biosynthesis 
                 0.00 
               
               
                 1424001_at 
                 Mki67ip 
                 1.88 
                 GO:0000398 
                 nuclear mRNA splicing, via spliceosome 
                 0.02 
               
               
                 1435544_at 
                 Exosc6 
                 1.87 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1425830_a_at 
                 2810452K22Rik 
                 1.87 
                 null 
                 unknownP 
                 0.33 
               
               
                 1426381_at 
                 Pprc1 
                 1.86 
                 GO:0000398 
                 nuclear mRNA splicing, via spliceosome 
                 0.02 
               
               
                 1438015_at 
                 BC068171 
                 1.84 
                 null 
                 unknownP 
                 0.33 
               
               
                 1451164_a_at 
                 Mrps18b 
                 1.82 
                 GO:0006412 
                 protein biosynthesis 
                 0.00 
               
               
                 1416890_at 
                 Wdr74 
                 1.81 
                 null 
                 unknownP 
                 0.33 
               
               
                 1415834_at 
                 Dusp6 
                 1.81 
                 GO:0006470 
                 protein amino acid dephosphorylation 
                 0.02 
               
               
                 1438527_at 
                 Rpl3 
                 1.79 
                 GO:0006412 
                 protein biosynthesis 
                 0.00 
               
               
                 1424151_at 
                 MGI: 2385237 
                 1.79 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1426554_a_at 
                 Pgam1 
                 1.79 
                 GO:0006096 
                 glycolysis 
                 0.04 
               
               
                 1455841_s_at 
                 Grwd1 
                 1.77 
                 null 
                 unknownP 
                 0.33 
               
               
                 1417873_at 
                 Pwp1 
                 1.75 
                 null 
                 unknownP 
                 0.33 
               
               
                 1452099_at 
                 AA408296 
                 1.75 
                 null 
                 unknownP 
                 0.33 
               
               
                 1422484_at 
                 Cycs 
                 1.74 
                 GO:0008635 
                 caspase activation via cytochrome c 
                 0.00 
               
               
                 1416070_a_at 
                 Ddx18 
                 1.74 
                 null 
                 unknownP 
                 0.33 
               
               
                 1435655_at 
                 Rpl12 
                 1.73 
                 GO:0007046 
                 ribosome biogenesis 
                 0.00 
               
               
                 1428390_at 
                 Wdr43 
                 1.72 
                 null 
                 unknownP 
                 0.33 
               
               
                 1434773_a_at 
                 Slc2a1 
                 1.71 
                 GO:0008643 
                 carbohydrate transport 
                 0.00 
               
               
                 1429268_at 
                 2610318N02Rik 
                 1.70 
                 null 
                 unknownP 
                 0.33 
               
               
                 1426958_at 
                 Rps9 
                 1.69 
                 GO:0006412 
                 protein biosynthesis 
                 0.00 
               
               
                 1437658_a_at 
                 Rnu22 
                 1.69 
                 null 
                 unknownP 
                 0.33 
               
               
                 1419518_at 
                 Tuba8 
                 1.69 
                 GO:0051258 
                 protein polymerization 
                 0.01 
               
               
                 1423703_at 
                 Ppan 
                 1.68 
                 GO:0001560 
                 regulation of cell growth by extracellular stimulus 
                 0.00 
               
               
                 1426931_s_at 
                 D19Bwg1357e 
                 1.67 
                 null 
                 unknownP 
                 0.33 
               
               
                 1418225_at 
                 Orc2l 
                 1.67 
                 GO:0006260 
                 DNA replication 
                 0.03 
               
               
                 1415802_at 
                 Slc16a1 
                 1.66 
                 GO:0015711 
                 organic anion transport 
                 0.00 
               
               
                 1423586_at 
                 Axl 
                 1.65 
                 GO:0000074 
                 regulation of cell cycle 
                 0.02 
               
               
                 1450387_s_at 
                 Ak3 
                 1.65 
                 GO:0006139 
                 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 
                 0.00 
               
               
                 1423884_at 
                 Cirh1a 
                 1.65 
                 null 
                 unknownP 
                 0.33 
               
               
                 1429897_a_at 
                 D16Ertd472e 
                 1.64 
                 null 
                 unknownP 
                 0.33 
               
               
                 1416445_at 
                 2810405J04Rik 
                 1.63 
                 null 
                 unknownP 
                 0.33 
               
               
                 1448480_at 
                 1110017C15Rik 
                 1.63 
                 GO:0007046 
                 ribosome biogenesis 
                 0.00 
               
               
                 1428970_at 
                 Mak3 
                 1.63 
                 null 
                 unknownP 
                 0.33 
               
               
                 1449886_a_at 
                 Timm9 
                 1.63 
                 GO:0006626 
                 protein-mitochondrial targeting 
                 0.00 
               
               
                 1456865_x_at 
                 Rrs1 
                 1.63 
                 GO:0007046 
                 ribosome biogenesis 
                 0.00 
               
               
                 1452902_at 
                 2610209N15Rik 
                 1.62 
                 GO:0008152 
                 metabolism 
                 0.05 
               
               
                 1423161_s_at 
                 Spred1 
                 1.60 
                 GO:0000188 
                 inactivation of MAPK 
                 0.00 
               
               
                 1448140_at 
                 Ciapin1 
                 1.60 
                 GO:0030097 
                 hemopoiesis 
                 0.02 
               
               
                 1426533_at 
                 Nol5a 
                 1.59 
                 GO:0007046 
                 ribosome biogenesis 
                 0.00 
               
               
                 1427997_at 
                 1110007M04Rik 
                 1.58 
                 null 
                 unknownP 
                 0.33 
               
               
                 1448450_at 
                 Ak2 
                 1.58 
                 GO:0006139 
                 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 
                 0.00 
               
               
                 1446771_at 
                 na 
                 1.57 
                 null 
                 unknownP 
                 0.33 
               
               
                 1452047_at 
                 Cacybp 
                 1.55 
                 GO:0006512 
                 ubiquitin cycle 
                 0.12 
               
               
                 1417064_at 
                 Jagn1 
                 1.55 
                 null 
                 unknownP 
                 0.33 
               
               
                 1424344_s_at 
                 Eif1a 
                 1.54 
                 null 
                 unknownP 
                 0.33 
               
               
                 1424473_at 
                 Polr2h 
                 1.54 
                 GO:0006350 
                 transcription 
                 0.14 
               
               
                 1433996_at 
                 Suv39h2 
                 1.54 
                 GO:0006333 
                 chromatin assembly or disassembly 
                 0.02 
               
               
                 1426394_at 
                 Eif3s1 
                 1.53 
                 GO:0006412 
                 protein biosynthesis 
                 0.00 
               
               
                 1428694_at 
                 5033413D16Rik 
                 1.53 
                 null 
                 unknownP 
                 0.33 
               
               
                 1434033_at 
                 Tle1 
                 1.53 
                 GO:0007222 
                 frizzled signaling pathway 
                 0.01 
               
               
                 1425921_a_at 
                 1810055G02Rik 
                 1.52 
                 null 
                 unknownP 
                 0.33 
               
               
                 1440120_at 
                 Gnb2l1 
                 1.52 
                 GO:0007205 
                 protein kinase C activation 
                 0.01 
               
               
                 1452094_at 
                 P4ha1 
                 1.52 
                 GO:0018401 
                 peptidyl-proline hydroxylation to 4-hydroxy-L-proline 
                 0.00 
               
               
                 1439071_at 
                 5430416N02Rik 
                 1.51 
                 null 
                 unknownP 
                 0.33 
               
               
                 1437007_x_at 
                 Usp39 
                 1.51 
                 GO:0006511 
                 ubiquitin-dependent protein catabolism 
                 0.01 
               
               
                 1416605_at 
                 Nola2 
                 1.51 
                 GO:0006412 
                 protein biosynthesis 
                 0.00 
               
               
                 1433576_at 
                 Mat2a 
                 1.51 
                 GO:0006556 
                 S-adenosylmethionine biosynthesis 
                 0.00 
               
               
                 1430127_a_at 
                 Ccnd2 
                 1.51 
                 GO:0000074 
                 regulation of cell cycle 
                 0.02 
               
               
                 1417675_a_at 
                 Mdn1 
                 1.51 
                 null 
                 unknownP 
                 0.33 
               
               
                 1429612_at 
                 Eml4 
                 1.50 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1450011_at 
                 Hsd17b12 
                 1.50 
                 GO:0006694 
                 steroid biosynthesis 
                 0.04 
               
               
                 1451254_at 
                 Ikbkap 
                 1.50 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1448563_at 
                 Phb 
                 1.50 
                 GO:0006259 
                 DNA metabolism 
                 0.04 
               
               
                 1432164_a_at 
                 Gcsh 
                 1.49 
                 GO:0006546 
                 glycine catabolism 
                 0.00 
               
               
                 1423730_at 
                 C130052I12Rik 
                 1.49 
                 null 
                 unknownP 
                 0.33 
               
               
                 1420056_s_at 
                 Ptdsr 
                 1.49 
                 GO:0006915 
                 apoptosis 
                 0.04 
               
               
                 1450914_at 
                 Ppp1r14b 
                 1.48 
                 null 
                 unknownP 
                 0.33 
               
               
                 1427578_a_at 
                 Itgb4bp 
                 1.47 
                 GO:0006412 
                 protein biosynthesis 
                 0.00 
               
               
                 1453745_at 
                 2700038G22Rik 
                 1.47 
                 null 
                 unknownP 
                 0.33 
               
               
                 1415807_s_at 
                 Sfrs2 
                 1.46 
                 GO:0000398 
                 nuclear mRNA splicing, via spliceosome 
                 0.02 
               
               
                 1447403_a_at 
                 Zmynd19 
                 1.46 
                 null 
                 unknownP 
                 0.33 
               
               
                 1451293_at 
                 Rnu3ip2 
                 1.46 
                 GO:0006364 
                 rRNA processing 
                 0.00 
               
               
                 1434574_at 
                 9430008C03Rik 
                 1.46 
                 null 
                 unknownP 
                 0.33 
               
               
                 1424545_at 
                 BC003965 
                 1.45 
                 null 
                 unknownP 
                 0.33 
               
               
                 1449044_at 
                 Eef1e1 
                 1.45 
                 GO:0006412 
                 protein biosynthesis 
                 0.00 
               
               
                 1435339_at 
                 Kctd15 
                 1.45 
                 null 
                 unknownP 
                 0.33 
               
               
                 1453195_at 
                 Sdccag3 
                 1.44 
                 null 
                 unknownP 
                 0.33 
               
               
                 1417132_at 
                 Cdc25a 
                 1.43 
                 GO:0000087 
                 M phase of mitotic cell cycle 
                 0.00 
               
               
                 1434398_at 
                 9430034D17Rik 
                 1.43 
                 GO:0006355 
                 regulation of transcription, DNA-dependent 
                 0.05 
               
               
                 1453983_a_at 
                 2810013M15Rik 
                 1.43 
                 null 
                 unknownP 
                 0.33 
               
               
                 1417233_at 
                 Chchd4 
                 1.43 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1448135_at 
                 Atf4 
                 1.43 
                 GO:0006094 
                 gluconeogenesis 
                 0.01 
               
               
                 1424942_a_at 
                 Myc 
                 1.42 
                 GO:0008633 
                 activation of pro-apoptotic gene products 
                 0.00 
               
               
                 1424019_at 
                 Nol1 
                 1.42 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1416962_at 
                 Rcc1 
                 1.42 
                 null 
                 unknownP 
                 0.33 
               
               
                 1429080_at 
                 Mphosph10 
                 1.42 
                 GO:0006364 
                 rRNA processing 
                 0.00 
               
               
                 1422844_a_at 
                 Wdr77 
                 1.41 
                 null 
                 unknownP 
                 0.33 
               
               
                 1419058_at 
                 Praf1 
                 1.41 
                 null 
                 unknownP 
                 0.33 
               
               
                 1423815_at 
                 Ddx56 
                 1.41 
                 GO:0006364 
                 rRNA processing 
                 0.00 
               
               
                 1416864_at 
                 Surf6 
                 1.41 
                 null 
                 unknownP 
                 0.33 
               
               
                 1416559_at 
                 1500003O22Rik 
                 1.40 
                 null 
                 unknownP 
                 0.33 
               
               
                 1434316_at 
                 Chsy1 
                 1.40 
                 GO:0030206 
                 chondroitin sulfate biosynthesis 
                 0.00 
               
               
                 1449348_at 
                 Mpp6 
                 1.40 
                 null 
                 unknownP 
                 0.33 
               
               
                 1450873_at 
                 Gtpbp4 
                 1.40 
                 GO:0007046 
                 ribosome biogenesis 
                 0.00 
               
               
                 1451459_at 
                 Ahctf1 
                 1.40 
                 null 
                 unknownP 
                 0.33 
               
               
                 1433530_at 
                 2210411K19Rik 
                 1.40 
                 null 
                 unknownP 
                 0.33 
               
               
                 1418571_at 
                 Tnfrsf12a 
                 1.39 
                 GO:0006931 
                 substrate-bound cell migration, cell attachment to substrate 
                 0.00 
               
               
                 1437238_x_at 
                 Nmd3 
                 1.39 
                 null 
                 unknownP 
                 0.33 
               
               
                 1428248_at 
                 Nfx1 
                 1.39 
                 GO:0045347 
                 negative regulation of MHC class II biosynthesis 
                 0.00 
               
               
                 1448617_at 
                 Cd53 
                 1.39 
                 null 
                 unknownP 
                 0.33 
               
               
                 1424227_at 
                 Polr3h 
                 1.39 
                 GO:0006101 
                 citrate metabolism 
                 0.00 
               
               
                 1433656_a_at 
                 Gnl3 
                 1.39 
                 null 
                 unknownP 
                 0.33 
               
               
                 1426939_at 
                 2310007F12Rik 
                 1.39 
                 null 
                 unknownP 
                 0.33 
               
               
                 1418079_at 
                 Psme3 
                 1.39 
                 null 
                 unknownP 
                 0.33 
               
               
                 1448126_at 
                 MGI: 1929091 
                 1.38 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1415733_a_at 
                 1110019J04Rik 
                 1.38 
                 null 
                 unknownP 
                 0.33 
               
               
                 1433880_at 
                 Dnajc11 
                 1.38 
                 GO:0006457 
                 protein folding 
                 0.01 
               
               
                 1417718_at 
                 Eif3s4 
                 1.38 
                 GO:0006412 
                 protein biosynthesis 
                 0.00 
               
               
                 1416563_at 
                 Ctps 
                 1.38 
                 GO:0006221 
                 pyrimidine nucleotide biosynthesis 
                 0.00 
               
               
                 1426311_s_at 
                 Zdhhc5 
                 1.37 
                 null 
                 unknownP 
                 0.33 
               
               
                 1416750_at 
                 Oprs1 
                 1.37 
                 null 
                 unknownP 
                 0.33 
               
               
                 1448568_a_at 
                 Slc20a1 
                 1.36 
                 GO:0006817 
                 phosphate transport 
                 0.04 
               
               
                 1452753_at 
                 Foxk2 
                 1.36 
                 null 
                 unknownP 
                 0.33 
               
               
                 1420463_at 
                 MGI: 1351468 
                 1.36 
                 GO:0007169 
                 transmembrane receptor protein tyrosine kinase signaling pathway 
                 0.07 
               
               
                 1425837_a_at 
                 Ccrn4l 
                 1.36 
                 GO:0048511 
                 rhythmic process 
                 0.01 
               
               
                 1434168_at 
                 Peo1 
                 1.36 
                 GO:0006268 
                 DNA unwinding 
                 0.00 
               
               
                 1416448_at 
                 Itpa 
                 1.36 
                 GO:0009117 
                 nucleotide metabolism 
                 0.02 
               
               
                 1434660_at 
                 Alkbh 
                 1.36 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1417035_at 
                 Sac3d1 
                 1.35 
                 null 
                 unknownP 
                 0.33 
               
               
                 1423480_at 
                 Nol11 
                 1.35 
                 null 
                 unknownP 
                 0.33 
               
               
                 1424436_at 
                 Gart 
                 1.35 
                 GO:0009113 
                 purine base biosynthesis 
                 0.00 
               
               
                 1450698_at 
                 Dusp2 
                 1.35 
                 GO:0006470 
                 protein amino acid dephosphorylation 
                 0.02 
               
               
                 1454659_at 
                 Dctd 
                 1.35 
                 GO:0006220 
                 pyrimidine nucleotide metabolism 
                 0.00 
               
               
                 1438198_at 
                 Bri3bp 
                 1.35 
                 null 
                 unknownP 
                 0.33 
               
               
                 1431182_at 
                 Hspa8 
                 1.34 
                 GO:0051085 
                 chaperone cofactor dependent protein folding 
                 0.00 
               
               
                 1426426_at 
                 Rbm13 
                 1.34 
                 null 
                 unknownP 
                 0.33 
               
               
                 1416126_at 
                 Rpo1-2 
                 1.34 
                 GO:0006350 
                 transcription 
                 0.14 
               
               
                 1424522_at 
                 Heatr1 
                 1.34 
                 null 
                 unknownP 
                 0.33 
               
               
                 1428244_at 
                 Larp1 
                 1.33 
                 null 
                 unknownP 
                 0.33 
               
               
                 1429456_a_at 
                 Polr3e 
                 1.33 
                 GO:0006350 
                 transcription 
                 0.14 
               
               
                 1456066_a_at 
                 Rpo1-4 
                 1.33 
                 GO:0006350 
                 transcription 
                 0.14 
               
               
                 1448178_a_at 
                 Cct3 
                 1.33 
                 GO:0006457 
                 protein folding 
                 0.01 
               
               
                 1451385_at 
                 2310056P07Rik 
                 1.33 
                 null 
                 unknownP 
                 0.33 
               
               
                 1440205_at 
                 na 
                 1.32 
                 null 
                 unknownP 
                 0.33 
               
               
                 1418566_s_at 
                 Nudcd2 
                 1.32 
                 null 
                 unknownP 
                 0.33 
               
               
                 1419030_at 
                 Ero1l 
                 1.32 
                 GO:0006457 
                 protein folding 
                 0.01 
               
               
                 1452203_at 
                 5830411E10Rik 
                 1.32 
                 GO:0006260 
                 DNA replication 
                 0.03 
               
               
                 1437052_s_at 
                 Slc2a3 
                 1.32 
                 GO:0008643 
                 carbohydrate transport 
                 0.00 
               
               
                 1417726_at 
                 Sssca1 
                 1.32 
                 null 
                 unknownP 
                 0.33 
               
               
                 1422767_at 
                 Bysl 
                 1.31 
                 GO:0007155 
                 cell adhesion 
                 0.34 
               
               
                 1423291_s_at 
                 Hyou1 
                 1.31 
                 GO:0006457 
                 protein folding 
                 0.01 
               
               
                 1452172_at 
                 2810421I24Rik 
                 1.31 
                 null 
                 unknownP 
                 0.33 
               
               
                 1437630_at 
                 D16Bwg1547e 
                 1.31 
                 null 
                 unknownP 
                 0.33 
               
               
                 1424244_at 
                 Rwdd4a 
                 1.31 
                 null 
                 unknownP 
                 0.33 
               
               
                 1417212_at 
                 9530058B02Rik 
                 1.31 
                 null 
                 unknownP 
                 0.33 
               
               
                 1428315_at 
                 Ebna1bp2 
                 1.31 
                 GO:0006364 
                 rRNA processing 
                 0.00 
               
               
                 1436007_a_at 
                 Thumpd1 
                 1.31 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1439027_at 
                 C330023M02Rik 
                 1.31 
                 null 
                 unknownP 
                 0.33 
               
               
                 1452012_a_at 
                 Exosc1 
                 1.31 
                 GO:0006364 
                 rRNA processing 
                 0.00 
               
               
                 1450986_at 
                 Nol5 
                 1.31 
                 GO:0006608 
                 snRNP protein-nucleus import 
                 0.00 
               
               
                 1423705_at 
                 2310057D15Rik 
                 1.30 
                 GO:0008152 
                 metabolism 
                 0.05 
               
               
                 1456738_s_at 
                 Brp16 
                 1.30 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1451884_a_at 
                 Lsm2 
                 1.30 
                 null 
                 unknownP 
                 0.33 
               
               
                 1421089_a_at 
                 2610028A01Rik 
                 1.30 
                 null 
                 unknownP 
                 0.33 
               
               
                 1451016_at 
                 Ifrd2 
                 1.30 
                 GO:0030154 
                 cell differentiation 
                 0.10 
               
               
                 1423841_at 
                 Bxdc2 
                 1.30 
                 null 
                 unknownP 
                 0.33 
               
               
                 1416022_at 
                 Fabp5 
                 1.30 
                 GO:0006656 
                 phosphatidylcholine biosynthesis 
                 0.00 
               
               
                 1423823_at 
                 2610012O22Rik 
                 1.30 
                 GO:0007046 
                 ribosome biogenesis 
                 0.00 
               
               
                 1448171_at 
                 Siah2 
                 1.30 
                 GO:000651 1 
                 ubiquitin-dependent protein catabolism 
                 0.01 
               
               
                 1448413_at 
                 2410016O06Rik 
                 1.29 
                 GO:0042254 
                 ribosome biogenesis and assembly 
                 0.00 
               
               
                 1456672_at 
                 AA408556 
                 1.29 
                 null 
                 unknownP 
                 0.33 
               
               
                 1416442_at 
                 Ier2 
                 1.29 
                 GO:0000004 
                 biological process unknown 
                 0.02 
               
               
                 1457083_at 
                 Prpf31 
                 1.29 
                 GO:0000351 
                 assembly of spliceosomal tri-snRNP U4/U6.U5 
                 0.00 
               
               
                 1448230_at 
                 Usp10 
                 1.29 
                 GO:0006511 
                 ubiquitin-dependent protein catabolism 
                 0.01 
               
               
                   
               
               
                             indicates data missing or illegible when filed 
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 3 
               
             
             
               
                   
               
               
                 48 genes/EST downregulated in fusion kinase-expressing Ba/F3 cells. 
               
               
                 Probe sets are ordered by increasing discriminating s           
               
             
          
           
               
                   
                   
                   
                   
                   
                 Onto- 
               
               
                   
                   
                 Discriminating 
                   
                   
                 Express P           
               
               
                 Probe Set 
                 Gene Symbol 
                 Score 
                 GO ID 
                 Onto-Express Biological Process 
                 value 
               
               
                   
               
             
          
           
               
                 1438038_at 
                 4930402H24Rik 
                 −2.301840428 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1459101_at 
                 C78760 
                 −1.937260526 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1430185_at 
                 5830460E08Rik 
                 −1.899962271 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1459557_at 
                 Zbtb16 
                 −1.889802945 
                 GO:0035136 
                 forelimb morphogenesis 
                 8.32E−05 
               
               
                 1425603_at 
                 0610011I04Rik 
                 −1.885885791 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1418411_at 
                 Fbxl8 
                 −1.884189604 
                 GO:0006512 
                 ubiquitin cycle 
                 3.08E−03 
               
               
                 1447901_x_at 
                 Sfi1 
                 −1.797938879 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1451115_at 
                 Pias3 
                 −1.778033499 
                 GO:0006512 
                 ubiquitin cycle 
                 3.08E−03 
               
               
                 1416538_at 
                 Ysg2 
                 −1.728551325 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1441885_s_at 
                 na 
                 −1.666293232 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1417896_at 
                 Tjp3 
                 −1.580284643 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1439857_at 
                 Usp32 
                 −1.555573141 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1449354_at 
                 U2af1-rs1 
                 −1.548084764 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1441319_at 
                 Rbm5 
                 −1.54504959 
                 GO:0000004 
                 biological process unknown 
                 9.65E−02 
               
               
                 1430896_s_at 
                 Nudt7 
                 −1.534925926 
                 GO:0015938 
                 coenzyme A catabolism 
                 2.08E−05 
               
               
                 1446598_at 
                 Prkca 
                 −1.532847936 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1447105_at 
                 na 
                 −1.518779997 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1424906_at 
                 Pqlc3 
                 −1.511859109 
                 nuil 
                 unknownP 
                 2.04E−01 
               
               
                 1442427_at 
                 9630026M06Rik 
                 −1.507828387 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1448104_at 
                 Aldh6a1 
                 −1.506711706 
                 GO:0008152 
                 metabolism 
                 1.28E−02 
               
               
                 1419557_a_at 
                 Tmem9 
                 −1.497471971 
                 GO:0006810 
                 transport 
                 2.31E−01 
               
               
                 1429351_at 
                 Klhl24 
                 −1.483148711 
                 nuil 
                 unknownP 
                 2.04E−01 
               
               
                 1434193_at 
                 Zmym6 
                 −1.457894796 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1434581_at 
                 na 
                 −1.455433574 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1417218_at 
                 2810048G17Rik 
                 −1.43831543 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1440897_at 
                 na 
                 −1.438296402 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1447112_s_at 
                 Cryl1 
                 −1.438004747 
                 GO:0006631 
                 fatty acid metabolism 
                 4.77E−03 
               
               
                 1434060_at 
                 Herc1 
                 −1.434063158 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1417066_at 
                 Cabc1 
                 −1.431967873 
                 GO:0006457 
                 protein folding 
                 2.98E−02 
               
               
                 1442315_at 
                 AI426778 
                 −1.428334819 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1438155_x_at 
                 Pigo 
                 −1.42673405 
                 GO:0009117 
                 nucleotide metabolism 
                 2.23E−03 
               
               
                 1433593_at 
                 Ypel5 
                 −1.42626537 
                 GO:0000004 
                 biological process unknown 
                 9.65E−02 
               
               
                 1455602_x_at 
                 C430010P07Rik 
                 −1.42303244 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1460257_a_at 
                 Mthfs 
                 −1.422588883 
                 G0:0008152 
                 metabolism 
                 1.28E−02 
               
               
                 1447738_s_at 
                 Ankrd13d 
                 −1.421336365 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1439079_a_at 
                 Erbb2ip 
                 −1.412999179 
                 GO:0006605 
                 protein targeting 
                 1.91E−02 
               
               
                 1429689_at 
                 4932433N03Rik 
                 −1.412810128 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1421948_a_at 
                 2610507L03Rik 
                 −1.397036044 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1438415_s_at 
                 Yipf2 
                 −1.390341353 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1425684_at 
                 2310005E10Rik 
                 −1.378218217 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1435345_at 
                 2600006K01Rik 
                 −1.375904328 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1434670_at 
                 Kif5a 
                 −1.361096401 
                 GO:0007018 
                 microtubule-based movement 
                 5.89E−03 
               
               
                 1424988_at 
                 Mylip 
                 −1.359416183 
                 GO:0006512 
                 ubiquitin cycle 
                 3.08E−03 
               
               
                 1428447_at 
                 Tmem14a 
                 −1.356743685 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1424621_at 
                 AA792894 
                 −1.355659364 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1448625_at 
                 Golga2 
                 −1.352622502 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1444235_at 
                 na 
                 −1.351686534 
                 null 
                 unknownP 
                 2.04E−01 
               
               
                 1440533_at 
                 Bfar 
                 −1.347482782 
                 GO:0006916 
                 anti-apoptosis 
                 5.98E−03 
               
               
                   
               
               
                             indicates data missing or illegible when filed