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Supplementary Table 1 Table 1. Genes that define an Rb null phenotype Rank Weight1 Fold Change2 Accession # Gene/description Function 1 2.02 17.97 AA008043 Cdc20 cell division cycle 20 homolog (S. cerevisiae) Mitosis 2 1.97 15.46 AA592163 3 1.88 14.13 Z21848 Pold1 DNA polymerase delta 1 DNA replication 4 1.86 19.69 x95351 Melk maternal embryonic leucine zipper kinase Signaling 5 1.84 10.6 Z46757 Hmgb2 high mobility group box 2 DNA packaging 6 1.84 11.96 d12513 Top2a topoisomerase II alpha DNA replication 7 1.78 16.82 AA117387 Knsl5 Kinesin-like 5 (mitotic kinesin-like protein 1) Mitosis 8 1.71 12.06 AA000468 Cdc20 cell division cycle 20 homolog (S. cerevisiae) Mitosis 9 1.64 12.33 C78700 10 1.64 8.63 u04674 Lig1 Dna ligase 1 DNA replication 11 1.62 8.84 AA008502 12 1.61 11.72 U25691 Hells lymphocyte specific helicase Lymphocyte proliferation 13 1.61 8.37 D86726 Mcmd6 Minichromosome maintenance deficient 6 (S. cerevisiae) DNA replication 14 1.59 9.62 m19438 Tk1 cytosolic thymidine kinase DNA replication 15 1.59 4.73 X15666 Rrm2 M2 subunit of mouse ribonucleotide reductase DNA replication 16 1.56 9.79 af002823 Bub1 mitotic checkpoint protein kinase (Bub1) Mitosis 17 1.55 9.29 D12513 Top2a DNA topoisomerase IIalpha fusion DNA replication 18 1.49 10.16 M86377 Ttk esk kinase Mitosis 19 1.47 7.95 D13473 Rad51 Rad51 protein. DNA repair 20 1.45 7.18 AA002747 21 1.44 8.95 D12646 Kif4 kif4 mRNA for microtubule-based motor protein Microtubule motor 22 1.43 7.69 X82786 Mki67 Ki-67. Mitosis 23 1.43 6.57 AA117100 Lag leukemia-associated gene Signaling 24 1.43 9.01 m31419 Ifi204 204 interferon-activatable protein Immune response 25 1.42 9.56 W98100 est 26 1.42 7.17 D26089 Mcmd4 Minichromosome maintenance deficient 4 (S. cerevisiae) DNA replication 27 1.4 6.55 AA215238 Slc29a1 Solute carrier family 29 (nucleoside transporters), member 1 Nucleoside transporter 28 1.37 6.79 X58708 CycB Cyclin B Mitosis 29 1.32 6.74 d13544 Prim1 primase small subunit DNA replication 30 1.31 6.4 AA426917 Ccnb1-rs1 cyclin B1- related sequence 1 Mitosis 31 1.3 6.23 m35153 Lmnb1 lamin B Cytoskeletal 32 1.3 5.91 AA689977 Mcmd6 Minichromosome maintenance deficient 6 DNA replication 33 1.29 6.79 AA238367 34 1.29 6.08 m14223 Rrm2 ribonucleotide reductase M2 subunit DNA replication 35 1.28 5.08 D26090 Mcmd5 Mini chromosome maintenance deficient 5 (S. cerevisiae) DNA replication 36 1.28 6.52 U42385 Fin16 fibroblast growth factor inducible gene 1 37 1.25 5.95 AA051276 38 1.24 6.19 AA266783 est 39 1.24 5.03 X66032 Ccnb2 cyclin B2. Mitosis 40 1.22 5.14 X53068 Pcna proliferating cell nuclear antigen. DNA replication 41 1.21 5.02 U58633 Cdc2a p34 cdc2 kinase mRNA Mitosis 42 1.17 5.26 AA049623 Racgap1 Rac GTPase activating protein 1 Signaling 43 1.15 5.35 AA268341 Ube2c Ubiquitin-conjugating enzyme E2C 44 1.14 4.87 D26091 Mcmd7 Minichromosome maintenance deficicient 7 (S. cerevisiae) DNA replication 45 1.14 4.61 D21099 Stk5 STK-1 (serine/threonine kinase) Signaling 46 1.14 4.89 C81593 Rrm2 ribonucleotide reductase M2 subunit DNA replication 47 1.13 4.35 X12944 Hmgn2 HMG-17 chromosomal protein. DNA packaging 48 1.11 4.52 C76791 Ris2 retroviral integration site 1 49 1.1 6.45 AB000121 Psmc3ip Proteasome 26S subunit, ATPase 3, interacting protein 50 1.1 4.95 Z31235 Lag leukemia-associated gene Signaling 51 1.08 4.6 C77497 52 1.05 3.73 X12944 Hmgn2 HMG-17 chromosomal protein DNA packaging 53 1.03 4.53 Y09632 Rab6kifl rabkinesin-6. vesicular transport 54 1.02 4.13 X64713 Ccnb1-rs1 cyclin B1, related sequence 1 Mitosis 55 1.01 4.46 AA718288 est 56 1 4.31 AA189300 est 57 0.996 5.69 C76145 est 58 0.99 4.3 AA590750 59 0.989 3.83 Z26580 Ccna2 cyclin A. Mitosis 60 0.967 4.38 W75122 61 0.965 4.16 K02927 Rrm1 ribonucleotide reductase M1 DNA replication 62 0.932 3.74 AC002393 Lcn7 lipocalin 7 63 0.897 3.65 AA059527 Nsg1 Neuron specific gene family member 1 membrane protein 64 0.847 3.34 U52951 Ezh2 enhancer of zeste homolog 2 transcription 65 0.836 3.59 l29479 Stk18 serine/threonine kinase 18 66 0.827 3.25 AA590750 67 0.795 3.27 AF004105 Mcmd2 Mini chromosome maintenance deficient 2 (S. cerevisiae) DNA replication 68 0.774 3.27 AA561108 Trip13 thyroid hormone receptor interactor 13 69 0.765 3.26 C78640 est 70 0.741 2.85 U63337 Cdk2 cyclin-dependent kinase 2 Mitosis 71 0.729 3.3 D00812 Rpa2 replication protein A2 DNA replication 72 0.724 2.97 AA285607 73 0.709 3.05 AA590400 74 0.707 2.83 AA407907 est 75 0.702 2.75 L06144 Plk polo-like kinase homolog, (Drosophila) signaling 76 0.676 2.8 W70733 Kifc5a kinesin family member C5A microtubule motor 77 0.671 3.11 U55041 Ung uracil-DNA glycosylase (ung) DNA repair 78 0.666 2.73 U19596 Cdkn2c cyclin-dependent kinase inhibitor 2C Cell cycle 79 0.666 2.4 X72310 Tfdp1 DP-1 heterodimer partner for E2Fs Cell cycle 80 0.612 2.41 U51167 Idh2 isocitrate dehydrogenase 2 metabolism 81 0.599 2.47 AA710868 82 0.541 2.48 AA182195 est 83 0.522 2.09 X13752 Alad aminolevulinate, delta dehydratase heme biosyn 84 0.51 2.14 AA269806 H2afx histone H2A, family member X DNA packaging 85 0.479 2 D67015 Impnb importin beta intracellular protein traffic 86 0.478 1.97 C77864 87 0.469 1.92 U89876 Refbp1 RNA and export factor binding protein 1 RNA metabolism 88 0.426 1.82 AA546958 est 89 0.393 1.69 AA117905 90 0.373 1.71 AA271012 Anapc5 anaphase promoting complexsubunit 5 Mitosis 91 0.37 1.7 AA271012 Anapc5 anaphase promoting complexsubunit 5 Mitosis 92 -0.481 0.54 AA274431 Sepr selenoprotein R 93 -0.573 0.5 AA015057 94 -0.615 0.49 C77861 Mvp major vault protein 95 -0.65 0.44 W08057 96 -0.913 0.35 C80271 Lcn7 lipocalin 7 97 -0.965 0.27 AA289858 Rnase4 ribonuclease 4 98 -1.14 0.23 J03482 H1f2 Mouse histone H1 gene, complete cds DNA packaging 99 -1.37 0.15 AA717972 est 100 -1.74 0.11 ET63372 1 The weight reflects the relative contribution to the discrimination based on the regression coefficient resulting from the factor analysis. 2 Fold change represents the mean expression value (average difference values) for the Rb samples divided by the mean expression value of the control samples..
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