Table 2.
Genes Showing Different Expression Between CR and NC Groups.
| A. Genes Showing Relatively Higher Expression in Radiosensitive Carcinoma Cells than in Radioresistant Cells | |||||||
| Category | Unigene ID (build #131) | Gene Symbol | Gene Name | U | CR/NC | P | Locus |
| DNA repair | Hs.3248 | MSH6 | mutS (E. coli) homolog 6 | 13 | 2.0 | 0.003 | 2p16 |
| Signal transduction | Hs.76578 | PIAS3 | protein inhibitor of activated STAT3 | 10 | 4.5 | 0.000 | 1q21 |
| Hs.29203 | GBL | G protein beta subunit-like | 11 | 2.8 | 0.044 | 16 | |
| Hs.479 | RAB5C | RAB5C, member RAS oncogene family | 12 | 2.8 | 0.001 | 17q21.2 | |
| Hs.28827 | MAP3K2 | mitogen-activated protein kinase kinase kinase 2 | 12 | 2.4 | 0.002 | 2 | |
| Hs.85155 | BRF1 | butyrate response factor 1 (EGF-response factor 1) | 14 | 2.4 | 0.003 | 14q22-q24 | |
| Hs.74615 | PDGFRA | platelet-derived growth factor receptor, alpha polypeptide | 14.5 | 3.3 | 0.023 | 4q11-q13 | |
| Hs.77439 | PRKAR2B | protein kinase, cAMP-dependent, regulatory, type II, beta | 15 | 5.9 | 0.009 | 7q22-q31.1 | |
| Hs.83070 | GRB14 | growth factor receptor-bound protein 14 | 17 | 9.8 | 0.042 | 2q22-q24 | |
| Transcription | Hs.66394 | RNF4 | ring finger protein 4 | 6 | 5.1 | 0.000 | 4p16.3 |
| Hs.8858 | BAZ1A | bromodomain adjacent to zinc finger domain, 1A | 9 | 5.0 | 0.031 | 14q12-q13 | |
| Hs.155321 | SRF | serum response factor (c-fos serum response element-binding transcription factor) | 9 | 2.0 | 0.038 | 6pter-6q15 | |
| Hs.289068 | TCF4 | transcription factor 4 | 15 | >2.2 | 0.048 | 18q21.1 | |
| Hs.760 | GATA2 | GATA-binding protein 2 | 15 | 2.0 | 0.011 | 3q21 | |
| Hs.316 | DDX6 | DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 | 16 | 3.3 | 0.009 | 11q23.3 | |
| Hs.301963 | HOXD8 | homeo box D8 | 17 | 3.3 | 0.038 | 2q31-q37 | |
| Hs.228059 | TIF1B | KRAB-associated protein 1 | 19 | 2.0 | 0.029 | 5 | |
| Adipogenesis | Hs.76392 | ALDH1 | aldehyde dehydrogenase 1, soluble | 15.5 | 14.1 | 0.018 | 9q21 |
| Hs.101850 | RBP1 | retinol-binding protein 1, cellular | 19 | 2.1 | 0.018 | 3q23 | |
| Cytoskeleton | Hs.7645 | FGB | fibrinogen, B beta polypeptide | 9 | 4.4 | 0.018 | 4q28 |
| Hs.75279 | LAMA2 | laminin, alpha 2 (merosin, congenital muscular dystrophy) | 10 | 5.2 | 0.040 | 6q22-q23 | |
| Hs.75445 | SPARCL1 | SPARC-like 1 (mast9, hevin) | 15 | 4.0 | 0.004 | 7 | |
| Hs.97266 | PCDH18 | protocadherin 18 | 16 | 5.9 | 0.006 | ||
| Hs.11494 | FBLN5 | fibulin 5 | 16 | 4.0 | 0.008 | 14q32.1 | |
| Hs.6441 | TIMP2 | tissue inhibitor of metalloproteinase 2 | 17 | 2.8 | 0.033 | 17q25 | |
| Hs.79914 | LUM | lumican | 17 | 2.2 | 0.035 | 12q21.3-q22 | |
| Hs.108896 | LOC51084 | lambda-crystallin | 18 | 4.7 | 0.022 | 13cen3q14.2 | |
| Hs.20072 | MIR | myosin regulatory light-chain interacting protein | 19 | 2.4 | 0.015 | 6p23-p22.3 | |
| Immune system | Hs.1244 | CD9 | CD9 antigen (p24) | 8 | 2.2 | 0.001 | 12p13 |
| Hs.74631 | BSG | basigin | 8 | 2.2 | 0.001 | 19p13.3 | |
| Hs.502 | ABCB3 | ATP-binding cassette, subfamily B (MDR/TAP), member 3 | 11 | 2.1 | 0.009 | 6p21.3 | |
| Hs.24395 | SCYB14 | small inducible cytokine subfamily B (Cys-X-Cys), member 14 (BRAK) | 17 | 5.0 | 0.007 | 5q31 | |
| Proteolysis | Hs.173091 | UBL3 | ubiquitin-like 3 | 15 | 2.5 | 0.016 | 13q12-q13 |
| Hs.75275 | UBE4A | ubiquitination factor E4A (homologous to yeast UFD2) | 19 | 3.8 | 0.047 | 11 | |
| Tumor related | Hs.81988 | DAB2 | disabled (Drosophila) homolog 2 (mitogen-responsive phosphoprotein) | 16 | 2.4 | 0.003 | 5p13 |
| Hs.75462 | BTG2 | BTG family, member 2 | 16 | 2.1 | 0.028 | 1q32 | |
| Peptide hormone | Hs.134932 | UCN | urocortin | 9 | 11.3 | 0.017 | 2p23-p21 |
| Others and ESTs | Hs.150926 | FPGT | fucose-phosphate guanylyltransferase | 10 | 2.1 | 0.009 | 1 |
| Hs.74566 | DPYSL3 | dihydropyrimidinase-like 3 | 18 | 2.6 | 0.015 | 5q32 | |
| Hs.101735 | DKFZP564J102 | DKFZP564J102 protein | 19 | 3.0 | 0.042 | 4 | |
| Hs.74571 | ARF1 | ADP-ribosylation factor 1 | 19 | 2.9 | 0.015 | 1q42 | |
| Hs.56874 | HSPB7 | heat shock 27-kDa protein family, member 7 (cardiovascular) | 4 | 2.5 | 0.005 | 1p36.23-p34.3 | |
| Hs.74376 | NOE1 | olfactomedin-related ER localized protein | 7 | 22.4 | 0.028 | 9 | |
| Hs.112569 | GAN | giant axonal neuropathy (gigaxonin) | 12 | 2.6 | 0.001 | 16q24.1 | |
| Hs.7535 | LOC55871 | COBW-like protein | 13 | 2.3 | 0.001 | 2 | |
| Hs.20597 | LCP | host cell factor homolog | 13 | 2.0 | 0.002 | ||
| Hs.24948 | SNCAIP | synuclein, alpha interacting protein (synphilin) | 14 | 7.0 | 0.003 | 5q23.1-q23.3 | |
| Hs.108725 | LOC51660 | HSPC040 protein | 15 | 3.0 | 0.005 | 6 | |
| Hs.49912 | LOC55895 | 22-kDa peroxisomal membrane protein-like | 15 | 2.7 | 0.015 | ||
| Hs.78103 | NAP1L4 | nucleosome assembly protein 1-like 4 | 17 | 7.0 | 0.009 | 11p15.5 | |
| Hs.111779 | SPARC | secreted protein, acidic, cys align="char"teine-rich (osteonectin) | 17 | 2.2 | 0.020 | 5q31.3-q32 | |
| Hs.75887 | COPA | coatomer protein complex, subunit alpha | 17 | 2.0 | 0.028 | 1q23-q25 | |
| Hs.129872 | SPAG9 | sperm-associated antigen 9 | 17 | 2.9 | 0.001 | 17 | |
| Hs.62041 | NID | nidogen (enactin) | 17 | 11.3 | 0.032 | 1q43 | |
| Hs.83834 | CYB5 | cytochrome b-5 | 18 | 3.6 | 0.040 | 18q23 | |
| Hs.29981 | SLC26A2 | solute carrier family 26 (sulfate transporter), member 2 | 19 | 2.8 | 0.001 | 5q31-q34 | |
| Hs.17930 | BING4 | BING4 | 19 | 2.9 | 0.000 | 6p21.3 | |
| Hs.6113 | STAU | staufen (Drosophila, RNA-binding protein) | 19 | 2.0 | 0.002 | 20q13.1 | |
| Hs.11951 | ENPP1 | ectonucleotide pyrophosphatase/phosphodiesterase 1 | 19.5 | >50 | 0.047 | 6q22-q23 | |
| Hs.172870 | ESTs | 4 | >50 | 0.000 | |||
| Hs.29664 | Human DNA sequence from clone 682J15 on chromosome 6p11.22.3. | 6 | 15.1 | 0.001 | |||
| Hs.12365 | KIAA1427 | KIAA1427 protein | 7 | >50 | 0.004 | ||
| Hs.107515 | ESTs | 7 | 3.5 | 0.000 | |||
| Hs.40583 | Homo sapiens clone TCBAP1028 mRNA sequence | 7 | 4.3 | 0.004 | |||
| Hs.115315 | ESTs | 7 | 2.2 | 0.037 | |||
| Hs.176092 | ESTs, moderately similar to myosin-binding protein H [H. sapiens] | 7 | 7.5 | 0.000 | |||
| Hs.125291 | ESTs | 7 | 10.0 | 0.000 | |||
| Hs.85053 | H. sapiens clone 24440 mRNA sequence | 8 | 11.2 | 0.000 | |||
| Hs.188228 | H. sapiens cDNA FLJ11003 fis, clone PLACE1002851 | 9 | 4.0 | 0.002 | |||
| Hs.296772 | Human DNA sequence from clone RP1-292B18 | 10 | 4.1 | 0.001 | |||
| Hs.83724 | Human clone 23773 mRNA sequence | 10 | 6.8 | 0.033 | |||
| Hs.124558 | EST | 10 | 2.8 | 0.008 | |||
| Hs.120399 | ESTs | 10 | 8.2 | 0.016 | |||
| Hs.116464 | ESTs | 11 | 3.4 | 0.014 | |||
| Hs.281434 | H. sapiens cDNA FLJ14028 fis, clone HEMBA1003838 | 11 | 2.9 | 0.031 | |||
| Hs.191271 | ESTs | 11 | 5.5 | 0.003 | |||
| Hs.26676 | FLJ10850 | hypothetical protein FLJ10850 | 11 | 4.8 | 0.004 | 20pter-20q12 | |
| Hs.292162 | ESTs | 11 | >50 | 0.007 | |||
| Hs.181304 | 13CDNA73 | putative gene product | 11 | >50 | 0.000 | 13 | |
| Hs.98265 | ESTs | 11 | 10.9 | 0.000 | |||
| Hs.126857 | H. sapiens cDNA FLJ12936 fis, clone NT2RP2005018 | 11 | 20.5 | 0.014 | |||
| Hs.95071 | ESTs | 11.5 | >50 | 0.001 | |||
| Hs.110373 | ESTs | 12 | 4.7 | 0.007 | |||
| Hs.114453 | ESTs | 12 | 2.6 | 0.005 | |||
| Hs.15725 | LOC51278 | hypothetical protein SBBI48 | 12 | 2.7 | 0.003 | 1p36.13q41 | |
| Hs.291979 | ESTs, Highly similar to pre-mRNA splicing SR protein rA4 | 12 | 4.6 | 0.019 | |||
| Hs.113082 | KIAA0443 | KIAA0443 gene product | 13 | 6.3 | 0.019 | X | |
| Hs.116117 | EST | 13 | 2.2 | 0.003 | |||
| Hs.24391 | H. sapiens cDNA FLJ13612 fis, clone PLACE1010833 | 13 | 5.9 | 0.034 | |||
| Hs.23120 | H. sapiens cDNA: FLJ21421 fis, clone COL04123 | 13 | 2.1 | 0.007 | |||
| Hs.116585 | ESTs | 13 | 2.0 | 0.014 | |||
| Hs.49476 | H. sapiens clone TUA8 Cri-du-chat region mRNA | 14 | 10.8 | 0.010 | |||
| Hs.112745 | EST | 14 | 2.1 | 0.029 | |||
| Hs.21851 | H. sapiens cDNA FLJ12900 fis, clone NT2RP2004321 | 14 | 2.7 | 0.001 | |||
| Hs.13809 | ESTs | 14 | 2.8 | 0.007 | |||
| Hs.61268 | ESTs | 14 | >50 | 0.032 | |||
| Hs.8469 | ESTs | 15 | 2.0 | 0.049 | |||
| Hs.11365 | H. sapiens cDNA FLJ12145 fis, clone MAMMA1000395 | 15 | 2.1 | 0.006 | |||
| Hs.107812 | ESTs, Weakly similar to SPOP [H. sapiens] | 15 | 2.8 | 0.027 | |||
| Hs.25329 | ESTs | 15 | 4.4 | 0.033 | |||
| Hs.178730 | ESTs | 16 | 2.3 | 0.000 | |||
| Hs.112607 | ESTs | 16 | 2.6 | 0.023 | |||
| Hs.27497 | H. sapiens cDNA FLJ11756 fis, clone HEMBA1005595 | 16 | 2.5 | 0.002 | |||
| Hs.29356 | ESTs | 16 | 2.0 | 0.024 | |||
| Hs.158688 | IF2 | KIAA0741 gene product | 16 | 4.6 | 0.042 | 2 | |
| Hs.23617 | FLJ20531 | hypothetical protein FLJ20531 | 17 | 2.8 | 0.041 | ||
| Hs.44159 | LOC51105 | CGI-72 protein | 17 | 13.7 | 0.003 | 8 | |
| Hs.23650 | ESTs, Weakly similar to AAB47496 NG5 [H. sapiens] | 17 | 3.3 | 0.041 | |||
| Hs.133081 | ESTs, Weakly similar to hypothetical protein [H. sapiens] | 17 | 24.6 | 0.011 | |||
| Hs.191379 | ESTs | 17 | 6.1 | 0.003 | |||
| Hs.72363 | H. sapiens mRNA for FLJ00116 protein, partial cds | 17.5 | >50 | 0.038 | |||
| Hs.173094 | H. sapiensmRNA; cDNA DKFZp564H142 (from clone DKFZp564H142) | 17.5 | 6.0 | 0.006 | |||
| Hs.179891 | ESTs, Weakly similar to prolyl 4-hydroxylase alpha subunit [H. sapiens] | 18 | 2.5 | 0.005 | |||
| Hs.22860 | ESTs | 18 | 2.3 | 0.011 | |||
| Hs.12867 | ESTs | 18 | 2.3 | 0.005 | |||
| Hs.200332 | FLJ20651 | hypothetical protein FLJ20651 | 18 | 3.8 | 0.004 | 9p24.1-9q22.33 | |
| Hs.273186 | LOC56997 | hypothetical protein, clone Telethon(Italy_B41)_Strait02270_FL142 | 18 | 2.8 | 0.041 | 1 | |
| Hs.30643 | ESTs | 18 | 5.7 | 0.018 | |||
| Hs.11805 | ESTs | 19 | 3.1 | 0.038 | |||
| Hs.22505 | FLJ10159 | hypothetical protein FLJ10159 | 19 | 2.7 | 0.025 | 6 | |
| Hs.127407 | ESTs | 19 | 5.6 | 0.011 | |||
| B. Genes Showing Relatively Higher Expression in Radioresistant Carcinoma Cells than in Radiosensitive Cells | |||||||
| Category | Unigene ID (build #131) | Gene Symbold | Gene Name | U | CR/NC | P | Locus |
| DNA repair | Hs.84981 | XRCC5 | X-ray repair complementing defective repair in Chinese hamster cells 5 | 73 | 0.39 | 0.034 | 2q35 |
| Signal transduction | Hs.155924 | CREM | cAMP responsive element modulator | 71 | 0.48 | 0.020 | 10p12.1-p11.1 |
| Hs.118520 | LOC55970 | G-protein gamma2 subunit | 73 | 0.40 | 0.015 | 1 | |
| Hs.34780 | DCX | doublecortex; lissencephaly, X-linked (doublecortin) | 74 | 0.48 | 0.012 | Xq22.3-q23 | |
| Hs.7138 | CHRM3 | cholinergic receptor, muscarinic 3 | 77 | 0.50 | 0.034 | 1q41-q44 | |
| Hs.250857 | CAMK2G | calcium/calmodulin-dependent protein kinase II gamma | 85 | 0.41 | 0.009 | 10q22 | |
| Transcription | Hs.168005 | TIF1GAMMA | transcriptional intermediary factor 1 gamma | 72 | 0.38 | 0.000 | 1p13.1 |
| Hs.21771 | WHSC2 | Wolf-Hirschhorn syndrome candidate 2 | 73 | 0.47 | 0.021 | 4p16.3 | |
| Hs.172280 | SMARCC1 | SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin | 74 | 0.38 | 0.005 | 3p23-p21 | |
| Hs.110457 | WHSC1 | Wolf-Hirschhorn syndrome candidate 1 | 78 | 0.45 | 0.005 | 4p16.3 | |
| Hs.78580 | DDX1 | DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 1 | 73 | 0.32 | 0.032 | 2p24 | |
| Translation | Hs.129673 | EIF4A1 | eukaryotic translation initiation factor 4A, isoform 1 | 78 | 0.43 | 0.001 | 17p13 |
| Glycolysis | Hs.2795 | LDHA | lactate dehydrogenase A | 75 | 0.39 | 0.036 | 11p15.4 |
| Cytoskeleton | Hs.821 | BGN | biglycan | 71 | 0.24 | 0.026 | Xq28 |
| Hs.172928 | COL1A1 | collagen, type I, alpha 1 | 74 | 0.46 | 0.007 | 17q21.3-q22 | |
| Hs.90408 | NEO1 | neogenin (chicken) homolog 1 | 78 | 0.48 | 0.006 | 15q22.3-q23 | |
| Immune system | Hs.516 | CCR1 | chemokine (C-C motif) receptor 1 | 71 | 0.28 | 0.039 | 3p21 |
| Hs.198253 | HLA-DQA1 | major histocompatibility complex, class II, DQ alpha 1 | 72.5 | 0.32 | 0.007 | 6p21.3 | |
| Hs.75498 | SCYA20 | small inducible cytokine subfamily A (Cys-Cys), member 20 | 73 | 0.18 | 0.041 | 2q33-q37 | |
| Hs.833 | ISG15 | interferon-stimulated protein, 15 kDa | 78 | 0.25 | 0.042 | 1 | |
| Proteolysis | Hs.61153 | PSMC2 | roteasome (prosome, macropain) 26S subunit, ATPase, 2 | 73 | 0.49 | 0.032 | 7q22.1-q22.3 |
| Apoptosis | Hs.93213 | BAK1 | BCL2-antagonist/killer 1 | 73 | 0.36 | 0.006 | 6p21.3 |
| Hs.278602 | API5 | apoptosis inhibitor 5 | 74 | 0.46 | 0.013 | 11 | |
| Others and ESTs | Hs.75593 | UROS | uroporphyrinogen III synthase | 71 | 0.13 | 0.041 | 10q25.2-q26.3 |
| Hs.108196 | LOC51659 | HSPC037 protein | 71 | 0.37 | 0.027 | 16 | |
| Hs.64595 | AASDHPPT | aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase | 71 | 0.44 | 0.033 | 11q22 | |
| Hs.286049 | PSA | phosphoserine aminotransferase | 72 | 0.47 | 0.009 | 9 | |
| Hs.93659 | ERP70 | protein disulfide isomerase-related protein | 73 | 0.26 | 0.036 | 10 | |
| Hs.2281 | CHGB | chromogranin B (secretogranin 1) | 75 | 0.31 | 0.011 | 20pter-p12 | |
| Hs.110099 | CBFA2T3 | core-binding factor, runt domain, alpha subunit 2; translocated to, 3 | 75 | 0.33 | 0.009 | 16q24 | |
| Hs.4747 | DKC1 | dyskeratosis congenita 1, dyskerin | 75 | 0.40 | 0.003 | Xq28 | |
| Hs.83848 | TPI1 | triosephosphate isomerase 1 | 77 | 0.43 | 0.040 | 12p13 | |
| Hs.75799 | PRSS8 | protease, serine, 8 (prostasin) | 77 | 0.13 | 0.045 | 16p11.2 | |
| Hs.143600 | GPP130 | type II Golgi membrane protein | 77 | 0.35 | 0.024 | 3 | |
| Hs.13565 | T-STAR | Sam68-like phosphotyrosine protein, T-STAR | 78 | 0.44 | 0.013 | 8q24.2 | |
| Hs.169476 | GAPD | glyceraldehyde-3-phosphate dehydrogenase | 80 | 0.47 | 0.042 | 12p13 | |
| Hs.114366 | PYCS | pyrroline-5-carboxylate synthetase | 87 | 0.24 | 0.006 | 10q24.3 | |
| Hs.43445 | PARN | poly(A)-specific ribonuclease (deadenylation nuclease) | 90 | 0.35 | 0.003 | 16p13 | |
| Hs.137556 | H. sapiens mRNA; cDNA DKFZp434A132 | 71 | 0.18 | 0.004 | |||
| Hs.65403 | LOC51323 | hypothetical protein | 71 | 0.50 | 0.003 | 6pter-6q15 | |
| Hs.164285 | ESTs, Weakly similar to Afg1p [S. cerevisiae] | 72 | 0.44 | 0.026 | |||
| Hs.26675 | ESTs | 74 | 0.32 | 0.012 | |||
| Hs.11641 | H. sapiens cDNA: FLJ21432 fis, clone COL04219 | 74 | 0.50 | 0.000 | |||
| Hs.14846 | H. sapiens mRNA; cDNA DKFZp564D016 | 75 | 0.38 | 0.009 | |||
| Hs.283127 | ESTs | 75 | 0.36 | 0.032 | |||
| Hs.63224 | ESTs | 75 | 0.16 | 0.038 | |||
| Hs.227591 | ESTs, Weakly similar to AF1488561 unknown [H. sapiens] | 76 | 0.50 | 0.017 | |||
| Hs.11156 | LOC51255 | hypothetical protein | 76 | 0.21 | 0.005 | 2 | |
| Hs.133207 | H. sapiens mRNA for KIAA1230 protein, partial cds | 77 | 0.42 | 0.011 | |||
| Hs.201925 | H. sapiens cDNA FLJ13446 fis, clone PLACE1002968 | 80 | 0.47 | 0.015 | |||
U, indicates Mann-Whitney statistics. CR/NC, difference ratio between median expression values for each group. P, permutational P value. Genes used for calculating predictive scores are noted in bold type.