The 64 genes selected by the permutation method
| Affymetrix probe no. . | HUGO name . | Description . | Unigene accession no. . |
|---|---|---|---|
| Signal transduction | |||
| 35665_at | PIK3C3** | phosphoinositide-3-kinase, class 3 | Hs.32971 |
| 37598_at | RASSF2 | Ras association (RalGDS/AF-6) domain family 2 | Hs.80905 |
| 1704_at | VAV2 | vav 2 oncogene | Hs.4248 |
| 38617_at | LIMK2 | LIM domain kinase 2 | Hs.278027 |
| 31389_at | OSIL | oxidative stress induced like | Hs.158298 |
| 32963_s_at | DKFZP761H171 | hypothetical GTP-binding protein DKFZp761H171 | Hs.238679 |
| 38018_g_at | CD79A | CD79A antigen (immunoglobulin-associated alpha) | Hs.79630 |
| 38767_at | SPRY1 | sprouty (Drosophila) homolog 1 (antagonist of FGF signaling) | Hs.88044 |
| 1692_s_at | GFRA2 | GDNF family receptor alpha 2 | Hs.19317 |
| 38749_at | GPR39 | G protein–coupled receptor 39 | Hs.85339 |
| Transcription | |||
| 39539_at | FBI-1* | HIV-1 inducer of short transcripts binding protein | Hs.104640 |
| 1915_s_at | FOS | v-fos FBJ murine osteosarcoma viral oncogene homolog | Hs.25647 |
| 1789_at | COPS5 | COP9 subunit 5 (Jun activation domain binding protein) | Hs.198767 |
| 37194_at | GATA2 | GATA-binding protein 2 | Hs.334695 |
| 1612_s_at | JUND** | jun D proto-oncogene | Hs.2780 |
| 2084_s_at | ETV4** | ets variant gene 4 (E1A enhancer-binding protein, E1AF) | Hs.77711 |
| Adhesion | |||
| 38976_at | CORO1A | coronin, actin-binding protein, 1A | Hs.109606 |
| 36958_at | ZYX | zyxin | Hs.75873 |
| 32594_at | CCT4 | chaperonin containing TCP1, subunit 4 (delta) | Hs.79150 |
| 1140_at | ITGAE | integrin, alpha E (antigen CD103) | Hs.851 |
| 1846_at | LGALS8 | lectin, galactoside-binding, soluble, 8 (galectin 8) | Hs.4082 |
| 31775_at | SFTPD | surfactant, pulmonary-associated protein D | Hs.253495 |
| 39657_at | KRT4** | keratin 4 | Hs.3235 |
| 33917_at | EPB41L1** | erythrocyte membrane protein band 4.1-like 1 | Hs.26395 |
| Apoptosis | |||
| 38281_at | CASP7** | caspase 7, apoptosis-related cysteine protease | Hs.9216 |
| 39688_at | REQ | requiem, apoptosis response zinc finger gene | Hs.13495 |
| Cell cycle/proliferation | |||
| 35688_g_at | MTCP1 | mature T-cell proliferation 1 | Hs.3548 |
| 36577_at | MIG2 | mitogen inducible 2 (cell cycle, cell proliferation) | Hs.75260 |
| 40139_at | FRAP1 | FK506 binding protein 12-rapamycin associated protein 1 | Hs.338207 |
| 218_at | IK | IK cytokine, down-regulator of HLA II | Hs.8024 |
| Ubiquit/trafficking | |||
| 40701_at | USP13** | ubiquitin specific protease 13 (isopeptidase T-3) | Hs.85482 |
| 40584_at | NUP88** | nucleoporin 88 kD | Hs.172108 |
| 35779_at | VPS45B** | vacuolar protein sorting 45B (yeast homolog) | Hs.6650 |
| 32234_at | DYT1 | dystonia 1, torsion (similar to heat-shock proteins, Clp proteases) | Hs.19261 |
| 31535_i_at | SEC23B | Sec23 (S. cerevisiae) homolog B (vesicle trafficking) | Hs.173497 |
| 688_at | PSMC1 | proteasome (prosome, macropain) 26S subunit, ATPase, 1 | Hs.4745 |
| 41076_at | GJB3 | gap junction protein, beta 3, 31 kD (connexin 31) | Hs.98485 |
| Metabolism | |||
| 33881_at | FACL3 | fatty-acid-Coenzyme A ligase, long-chain 3 | Hs.268012 |
| 37355_at | MLN64 | steroidogenic acute regulatory protein related | Hs.77628 |
| 40963_at | ABCA4** | ATP-binding cassette, subfamily A (ABC1), member 4 | Hs.198396 |
| 37033_s_at | GPX1 | glutathione peroxidase 1 | Hs.76686 |
| 31816_at | GAA | glucosidase, alpha; acid | Hs.1437 |
| 38529_at | ACACB | acetyl-Coenzyme A carboxylase beta | Hs.183857 |
| 33568_at | CHRNB4 | cholinergic receptor, nicotinic, beta polypeptide 4 | Hs.54397 |
| Miscellaneous | |||
| 33060_g_at | NULL | Homo sapiens clone 24820 mRNA sequence | Hs.146312 |
| 36375_at | ODF1* | outer dense fibre of sperm tails 1 | Hs.159274 |
| 32913_i_at | LOC58509 | NY-REN-24 antigen | Hs.128425 |
| 33464_at | NULL | Homo sapiens mRNA full-length cDNA clone EUROIMAGE 25206 | Hs.25314 |
| 39229_at | SDCCAG1 | serologically defined colon cancer antigen 1 | Hs.54900 |
| 39784_at | EIF2S1 | eukaryotic translation initiation factor 2, subunit 1 (alpha, 35kD) | Hs.151777 |
| 36971_at | KIAA0257 | KIAA0257 protein | Hs.75912 |
| 37036_at | KIAA0301 | KIAA0301 protein | Hs.76730 |
| 32646_at | KIAA0449 | KIAA0449 protein | Hs.169182 |
| 41134_at | KIAA0964 | KIAA0964 protein | Hs.177425 |
| 40223_r_at | KIAA0685 | KIAA0685 gene product | Hs.296406 |
| 35260_at | MONDOA* | KIAA0867 protein | Hs.52081 |
| 38728_at | KIAA0225 | KIAA0225 protein | Hs.84790 |
| 32556_at | U2AF65 | U2 small nuclear ribonucleoprotein auxiliary factor (65 kD) | Hs.7655 |
| 1532_g_at | NULL | Human BRCA2 region, mRNA sequence CG006 | Hs.110630 |
| 32502_at | NULL | Homo sapiens clone PP1665 unknown mRNA | Hs.6748 |
| 34703_f_at | NULL | ESTs, Highly similar to ORF2 [H.sapiens] | Hs.323782 |
| 31414_at | TTY2** | testis-specific testis transcript Y 2 | Hs.158345 |
| 37885_at | AF038169 | hypothetical protein | Hs.145567 |
| 36398_at | NULL | ESTs, Moderately similar to POL2_HUMAN RETROVIRUS | Hs.163863 |
| Affymetrix probe no. . | HUGO name . | Description . | Unigene accession no. . |
|---|---|---|---|
| Signal transduction | |||
| 35665_at | PIK3C3** | phosphoinositide-3-kinase, class 3 | Hs.32971 |
| 37598_at | RASSF2 | Ras association (RalGDS/AF-6) domain family 2 | Hs.80905 |
| 1704_at | VAV2 | vav 2 oncogene | Hs.4248 |
| 38617_at | LIMK2 | LIM domain kinase 2 | Hs.278027 |
| 31389_at | OSIL | oxidative stress induced like | Hs.158298 |
| 32963_s_at | DKFZP761H171 | hypothetical GTP-binding protein DKFZp761H171 | Hs.238679 |
| 38018_g_at | CD79A | CD79A antigen (immunoglobulin-associated alpha) | Hs.79630 |
| 38767_at | SPRY1 | sprouty (Drosophila) homolog 1 (antagonist of FGF signaling) | Hs.88044 |
| 1692_s_at | GFRA2 | GDNF family receptor alpha 2 | Hs.19317 |
| 38749_at | GPR39 | G protein–coupled receptor 39 | Hs.85339 |
| Transcription | |||
| 39539_at | FBI-1* | HIV-1 inducer of short transcripts binding protein | Hs.104640 |
| 1915_s_at | FOS | v-fos FBJ murine osteosarcoma viral oncogene homolog | Hs.25647 |
| 1789_at | COPS5 | COP9 subunit 5 (Jun activation domain binding protein) | Hs.198767 |
| 37194_at | GATA2 | GATA-binding protein 2 | Hs.334695 |
| 1612_s_at | JUND** | jun D proto-oncogene | Hs.2780 |
| 2084_s_at | ETV4** | ets variant gene 4 (E1A enhancer-binding protein, E1AF) | Hs.77711 |
| Adhesion | |||
| 38976_at | CORO1A | coronin, actin-binding protein, 1A | Hs.109606 |
| 36958_at | ZYX | zyxin | Hs.75873 |
| 32594_at | CCT4 | chaperonin containing TCP1, subunit 4 (delta) | Hs.79150 |
| 1140_at | ITGAE | integrin, alpha E (antigen CD103) | Hs.851 |
| 1846_at | LGALS8 | lectin, galactoside-binding, soluble, 8 (galectin 8) | Hs.4082 |
| 31775_at | SFTPD | surfactant, pulmonary-associated protein D | Hs.253495 |
| 39657_at | KRT4** | keratin 4 | Hs.3235 |
| 33917_at | EPB41L1** | erythrocyte membrane protein band 4.1-like 1 | Hs.26395 |
| Apoptosis | |||
| 38281_at | CASP7** | caspase 7, apoptosis-related cysteine protease | Hs.9216 |
| 39688_at | REQ | requiem, apoptosis response zinc finger gene | Hs.13495 |
| Cell cycle/proliferation | |||
| 35688_g_at | MTCP1 | mature T-cell proliferation 1 | Hs.3548 |
| 36577_at | MIG2 | mitogen inducible 2 (cell cycle, cell proliferation) | Hs.75260 |
| 40139_at | FRAP1 | FK506 binding protein 12-rapamycin associated protein 1 | Hs.338207 |
| 218_at | IK | IK cytokine, down-regulator of HLA II | Hs.8024 |
| Ubiquit/trafficking | |||
| 40701_at | USP13** | ubiquitin specific protease 13 (isopeptidase T-3) | Hs.85482 |
| 40584_at | NUP88** | nucleoporin 88 kD | Hs.172108 |
| 35779_at | VPS45B** | vacuolar protein sorting 45B (yeast homolog) | Hs.6650 |
| 32234_at | DYT1 | dystonia 1, torsion (similar to heat-shock proteins, Clp proteases) | Hs.19261 |
| 31535_i_at | SEC23B | Sec23 (S. cerevisiae) homolog B (vesicle trafficking) | Hs.173497 |
| 688_at | PSMC1 | proteasome (prosome, macropain) 26S subunit, ATPase, 1 | Hs.4745 |
| 41076_at | GJB3 | gap junction protein, beta 3, 31 kD (connexin 31) | Hs.98485 |
| Metabolism | |||
| 33881_at | FACL3 | fatty-acid-Coenzyme A ligase, long-chain 3 | Hs.268012 |
| 37355_at | MLN64 | steroidogenic acute regulatory protein related | Hs.77628 |
| 40963_at | ABCA4** | ATP-binding cassette, subfamily A (ABC1), member 4 | Hs.198396 |
| 37033_s_at | GPX1 | glutathione peroxidase 1 | Hs.76686 |
| 31816_at | GAA | glucosidase, alpha; acid | Hs.1437 |
| 38529_at | ACACB | acetyl-Coenzyme A carboxylase beta | Hs.183857 |
| 33568_at | CHRNB4 | cholinergic receptor, nicotinic, beta polypeptide 4 | Hs.54397 |
| Miscellaneous | |||
| 33060_g_at | NULL | Homo sapiens clone 24820 mRNA sequence | Hs.146312 |
| 36375_at | ODF1* | outer dense fibre of sperm tails 1 | Hs.159274 |
| 32913_i_at | LOC58509 | NY-REN-24 antigen | Hs.128425 |
| 33464_at | NULL | Homo sapiens mRNA full-length cDNA clone EUROIMAGE 25206 | Hs.25314 |
| 39229_at | SDCCAG1 | serologically defined colon cancer antigen 1 | Hs.54900 |
| 39784_at | EIF2S1 | eukaryotic translation initiation factor 2, subunit 1 (alpha, 35kD) | Hs.151777 |
| 36971_at | KIAA0257 | KIAA0257 protein | Hs.75912 |
| 37036_at | KIAA0301 | KIAA0301 protein | Hs.76730 |
| 32646_at | KIAA0449 | KIAA0449 protein | Hs.169182 |
| 41134_at | KIAA0964 | KIAA0964 protein | Hs.177425 |
| 40223_r_at | KIAA0685 | KIAA0685 gene product | Hs.296406 |
| 35260_at | MONDOA* | KIAA0867 protein | Hs.52081 |
| 38728_at | KIAA0225 | KIAA0225 protein | Hs.84790 |
| 32556_at | U2AF65 | U2 small nuclear ribonucleoprotein auxiliary factor (65 kD) | Hs.7655 |
| 1532_g_at | NULL | Human BRCA2 region, mRNA sequence CG006 | Hs.110630 |
| 32502_at | NULL | Homo sapiens clone PP1665 unknown mRNA | Hs.6748 |
| 34703_f_at | NULL | ESTs, Highly similar to ORF2 [H.sapiens] | Hs.323782 |
| 31414_at | TTY2** | testis-specific testis transcript Y 2 | Hs.158345 |
| 37885_at | AF038169 | hypothetical protein | Hs.145567 |
| 36398_at | NULL | ESTs, Moderately similar to POL2_HUMAN RETROVIRUS | Hs.163863 |
The mRNAs from Fn- or PLL-stimulated cells were analyzed by Hu95av2 microarrays as described in “Materials and methods.” Data were then analyzed with D-Chip software. Genes were selected if an expression of more than 100 was reached for at least one time point in one condition. Genes are classified by biological functions. Forty-six of the 64 genes overlap with the 72 genes selected by assuming normality (designated by shading in the first column). One asterisk (*) indicates that the same gene has also been selected at 24 or 48 hours; two asterisks (**), that a relative gene (same family or other subunit) has also been selected at 24 or 48 hours.