Table 1.
The list of 36 genes forming the minimal signature as defined by PAM analysis
| Accession number | Gene Name | PAM Occur | SAM score (R/RF) | Fold-Change (R/RF) | Gene Title | Functional pathway |
|---|---|---|---|---|---|---|
| NM_017761 | PNRC2* | 0.98 | −3.67 | 0.60 | Proline-rich nuclear receptor coactivator 2 | ER activity regulation |
| AK027663 | STC2* | 0.98 | −3.36 | 0.43 | Stanniocalcin 2 | Cell growth |
| NM_014736 | KIAA0101/p15(PAF)* | 0.97 | 3.46 | 1.69 | PCNA-associated factor | DNA repair; Anti-apoptosis |
| NM_000165 | GJA1/CX43* | 0.96 | −3.04 | 0.45 | Gap junction protein, alpha 1, 43kDa (connexin 43) | Cell growth; Adhesion; Apoptosis |
| BC015719 | OTUD7B* | 0.94 | −3.03 | 0.60 | OTU domain containing 7B | Signalisation; Inflammation |
| AK023933 | ZBTB44* | 0.92 | −2.70 | 0.69 | Zinc finger and BTB domain-containing protein 44 function | Unknown |
| NM_018154 | ASF1B* | 0.89 | 3.29 | 1.67 | ASF1 anti-silencing function 1 homolog B (S. cerevisiae) | DNA repair |
| AL137566 | - | 0.89 | −2.87 | 0.54 | - | - |
| AF085233 | SGK3/SGKL* | 0.89 | −2.52 | 0.51 | Serum/glucocorticoid regulated kinase 3 | Signalisation |
| NM_002421 | MMP1 | 0.88 | 2.79 | 2.27 | Matrix metalloproteinase 1 | Invasion |
| NM_004701 | CCNB2* | 0.88 | 2.78 | 1.43 | Cyclin B2 | Mitosis; Cell cycle |
| NM_006103 | WFDC2/HE4 | 0.87 | −3.07 | 0.45 | WAP four-disulfide core domain 2; Epididymal secretory protein E4 | Immune response |
| NM_012112 | TPX2* | 0.84 | 3.04 | 1.54 | Microtubule-associated homolog (Xenopus laevis) | Mitosis; Cell cycle |
| NM_001034 | RRM2* | 0.84 | 2.81 | 1.69 | Ribonucleotide reductase M2 polypeptide | DNA repair |
| NM_017680 | ASPN/SLRR1C | 0.83 | −2.46 | 0.46 | Asporin; Small leucine-rich repeat class 1 | Adhesion |
| NM_006197 | PCM1* | 0.82 | −3.04 | 0.56 | Pericentriolar material 1 | Cell growth; Mitosis |
| NM_007019 | UBE2C/UBCH10* | 0.82 | 2.85 | 1.49 | E2 ubiquitin-conjugating enzyme | Mitosis; Cell cycle |
| NM_004217 | AURKB/STK12* | 0.80 | 3.07 | 1.52 | Aurora B kinase | Mitosis; Cell cycle |
| NM_001461 | FMO5* | 0.78 | −2.52 | 0.57 | Flavin containing monooxygenase 5 | Metabolism |
| AF326917 | AUTS2* | 0.77 | −2.70 | 0.57 | Autism susceptibility candidate 2 | Unknown function |
| NM_014056 | HIGD1A/HIG1* | 0.76 | −2.97 | 0.49 | HIG1 domain family, member 1A; Hypoxia-inducible gene 1 | Anti-apoptosis |
| NM_003981 | PRC1* | 0.74 | 3.04 | 1.56 | Protein regulator of cytokinesis 1 | Mitosis; Cell cycle |
| AK001379 | ASPM* | 0.73 | 2.98 | 1.61 | Abnormal spindle-like microcephaly-associated protein | Mitosis; Cell cycle |
| AB033114 | MTUS1/ATIP1* | 0.72 | −2.78 | 0.63 | Mitochondrial tumor suppressor 1; Angiotensin II receptor-interacting protein | Cell growth; Signalisation |
| AL133047 | SH3D19* | 0.72 | −2.90 | 0.65 | SH3 domain protein D19 | Signalisation |
| NM_006570 | RRAGA* | 0.72 | −3.37 | 0.63 | Ras-related GTP-binding A | Signalisation |
| NM_032471 | PKIB | 0.70 | −2.57 | 0.47 | Protein kinase A inhibitor beta | ER activity regulation; Signalisation |
| NM_016441 | CRIM1* | 0.68 | −2.34 | 0.65 | Cysteine-rich motor neuron 1; Cysteine rich transmembrane BMP regulator 1 | Adhesion |
| AF444143 | SPG3A/ATL1* | 0.68 | −2.83 | 0.55 | Atlastin-1; Spastic paraplegia 3A; GTP-binding protein 3 | Signalisation; Vesicle trafficking |
| NM_021999 | ITM2B/BRI2* | 0.67 | −2.98 | 0.60 | Integral membrane protein 2B; Transmembrane protein BRI | Apoptosis |
| NM_020038 | ABCC3/MRP3 | 0.65 | 2.72 | 2.04 | ATP-binding cassette, sub-family C (CFTR/MRP) member | Multidrug resistance |
| NM_005824 | LRRC17/P37NB* | 0.65 | −2.30 | 0.60 | Leucine rich repeat containing 17 | Unknown function |
| NM_020347 | LZTFL1* | 0.64 | −2.71 | 0.69 | Leucine zipper transcription factor-like 1 | Unknown function |
| NM_003890 | FCGBP | 0.64 | −2.45 | 0.53 | Fc fragment IgG binding protein | Immune response |
| NM_003258 | TK1* | 0.63 | 2.43 | 1.33 | Thymidine kinase 1 | DNA replication |
| NM_001786 | CDC2/CDK1* | 0.63 | 2.43 | 1.32 | Cell division cycle 2, G1 to S and G2 to M; Cyclin-dependent kinase 1 | Mitosis; Cell cycle |
Genes present in more than 60% of the 100 PAM iterative signatures are listed and the respective occurrence values (PAM Occur) are indicated. SAM scores and Fold-changes defined upon SAM analysis are indicated (R, patients with relapse; RF, relapse-free patients). Genes with a minimum 1.51 fold-change and a SAM score ≥ ± 2.52 are in bold characters. Genes were overexpressed in R tumors when fold-change was ≥ 1 and down-regulated when fold-change was ≤ 1. Genes that are common to the PAM and to the KNN signatures are marked with a star (*).