Table 1.
List of 35 genes selected using the criteria illustrated in Fig. 1b
| Probe set ID | Gene symbol | Gene ontology bio process, cell component, molecular function | Correlation | P value |
|---|---|---|---|---|
| Pattern 1 (6 genes) | ||||
| M22898_at | TP53 | Apoptosis, cell cycle checkpoint, DNA repair, transcription factor, tumor suppressor | 0.9858 | 0.0003 |
| K02766_at | C9 | Complement component, hemolysin | 0.9315 | 0.0069 |
| U44429_at | TPD52L1 | Oncogenesis | 0.9113 | 0.0114 |
| M16987_at | F5 | Blood coagulation | 0.8894 | 0.0177 |
| M64358_at | RHOM3A | Unknown function | 0.888 | 0.0181 |
| M26061_at | PDE6A | Vision, cGMP-specific phosphodiesterase | 0.8653 | 0.026 |
| Pattern 2 (1 gene) | ||||
| X82539_at | MAGEB1 | Tumor antigen | 0.0416 | |
| Pattern 3 (21 genes) | ||||
| U16306_at | CSPG2 | Cell adhesion, developmental processes, cell recognition | 0.0002 | |
| M96843_at | ID2B | Dominant-negative helix–loop–helix transcription factor, DNA binding, protein binding, developmental processes | 0.0041 | |
| L25798_at | HMGCS1 | Lipid metabolism | 0.0085 | |
| X57025_at | IGF1 | Signal transduction, positive control of cell proliferation, cell motility | 0.0135 | |
| D82345_at | TMSNB | Unknown function | 0.0164 | |
| U12535_at | EPS8 | Signal transduction, cell proliferation, EGF receptor signaling pathway, SH3/SH2 adaptor protein | 0.0169 | |
| Z25521_s_at | CD47 | Signal transduction | 0.0199 | |
| L22075_at | GNA13 | Signal transduction, cell motility, heterotrimeric G-protein GTPase, α subunit | 0.0237 | |
| U18242_at | CAMLG | Signal transduction, defense response | 0.0243 | |
| L19871_at | ATF3 | Cell-matrix adhesion, integrin-mediated signaling pathway, oncogenesis, transcription corepressor | 0.0305 | |
| S41458_at | PDE6B | Phototransduction, visible light, vision, cGMP-specific phosphodiesterase | 0.0316 | |
| M86852_at | PXMP3 | Protein-peroxisome, targeting peroxisome, organization, and biogenesis | 0.034 | |
| Y11897_at | CHIC1 | Unknown function | 0.0359 | |
| U44772_at | PPT1 | Neurogenesis | 0.036 | |
| U63295_at | SIAH1 | Axon guidance, embryogenesis and morphogenesis, apoptosis, neurogenesis | 0.0378 | |
| X05997_at | LIPF | Hydrolase, lipid degradation, glycoprotein | 0.0387 | |
| X66087_at | MYBL1 | Transcription regulation from Pol II promoter, transcription-activating factor | 0.04 | |
| Y08991_at | PIK3R4 | Nonselective vesicle transport enzyme activator | 0.0409 | |
| Z46788_at | CYLC2 | Cell shape, cell size control, cytoskeletal structural protein | 0.0434 | |
| Z15108_at | PIKCZ | Antiapoptosis, signal transduction, protein phosphorylation, protein kinase | 0.0436 | |
| D87127_at | TLOC1 | Cotranslational membrane targeting | 0.0483 | |
| Pattern 4 (3 genes) | ||||
| AB000220_at | SEMA3C | Axon guidance, cell growth and maintenance, immune response, drug resistance | −0.9711 | 0.0012 |
| M60047_at | HBP17 | Signal transduction, negative control of cell proliferation, cell–cell signaling, heparin binding | −0.8764 | 0.022 |
| X02874_at | OAS1 | Nucleobase, nucleoside, nucleotide, and nucleic acid metabolism | −0.8326 | 0.0397 |
| Pattern 5 (2 genes) | ||||
| D38491_at | KIAA0117 | RNA-binding protein | 0.0019 | |
| U11313_at | SCP2 | Acyl-CoA metabolism, peroxisome organization and biogenesis, sterol carrier protein X-related thiolase | 0.0085 | |
| Pattern 6 (2 genes) | ||||
| U67988_at | DLGAP1 | Synaptic transmission protein binding | 0.0089 | |
| U79289_at | LOC148357 | Unknown function | 0.0094 | |
| Known targets | ||||
| U33202_s_at | MDM2 | Negative control of cell proliferation oncogenesis | 0.8824 | 0.0199 |
| U33203_s_at | MDM2 | Negative control of cell proliferation oncogenesis | 0.8821 | 0.02 |
| U09579_at | CDKN1A | Induction of apoptosis, cell cycle arrest, negative control of cell proliferation, regulation of CDK activity | 0.8785 | 0.0213 |
*
Gene annotation based on the GeneOntology Consortium (www.geneontology.org) and Affymetrix (www.affymetrix.com/analysis/index.affx).
†
Pearson's correlation coefficient for correlation with p53 status.
‡
Genes with P values <0.05 were considered. Known p53 target genes that show a high correlation with p53 status but did not meet the threshold criteria are reported at the bottom.