Table 1.
Selected genes from top liver-specific RB-loss gene signature GO term clusters
| Representative GO Term (ID) | Selected Genes | Enrichment Score | P-value |
|---|---|---|---|
| Upregulated | |||
| Cluster 1: Cell cycle (0007049) | HAUS8, DSN1, E2F1, E2F2, H2AFX, RAD21, AURKA, AURKB, ANAPC4, BRCA2, CDC5, CENPE, CCNA2, CDK2, INCENP, MCM7, MDM2, MYB, PIN1, PLK1 | 51.77 | 1.4E-74 |
| Cluster 2: DNA metabolic process (0006259) | ASF1A, BLM, DNMT1, APAF1, BRCA1, BRCA2, CHEK1, CCNE1, POLA1, RBBP7, PARP1, TOP2A | 22.37 | 1.5E-40 |
| Cluster 3: M phase of meiotic cell cycle (0051327) | FBXO43, FBXO5, NEK2, EXO1, PTTG1, SMC3, TRIP13, TOPBP1 | 9.72 | 1.7E-11 |
| Cluster 4: Microtubule cytoskeleton organization (0000226) | HAUS1, HAUS4, BIRC5, KIF11, RANBP1, CENPE, CENPJ, CKAP5 | 9.23 | 1.7E-13 |
| Cluster 5: Chromosome organization (0051276) | ASF1A, DNMT1, H1FX, CBX6, CDCA5, HAT1, HELLS, NUSAP1 | 5.76 | 1.1E-14 |
| Downregulated | |||
| Cluster 1: Immune response (0006955) | BCL3, CD14, CD74, CCL2, CCL5, CXCL1, CFP, IGJ, IL1B, NLRP3, TLR2, TLR4, TLR7, TGFB1 | 10.06 | 2.1E-12 |
| Cluster 2: Taxis (0042330) | FCER1G, RAC2, S100A9, CCL2, CCL5, CXCL10, C5AR1, FPR1, ITGB2, | 5.78 | 4.5E-9 |
| Cluster 3: Activation of immune response (0002253) | CD3E, FCER1G, C1QA, C1QB, MASP1, NFKBIA, PLCG2, PTPRC | 3.94 | 1.8E-6 |
| Cluster 4: Response to molecule of bacterial origin (0002237) | CD14, C5AR1, IL1B, PLCG2, SLC11A1, TLR2, TLR4 | 3.75 | 1.4E-5 |
| Cluster 5: Enzyme linked receptor protein signaling pathway (0007167) | ARAP1, AXL, SMAD7, CSF1R, CTGF, FOXC2, ID1, PDGFRA, TGFBR3 | 3.35 | 2.6E-4 |
Genes selected from the top liver-specific RB-loss gene signature annotation clusters represent both increased (cellular proliferation) and decreased (immune function) processes. Expression of all selected genes was significantly different between groups as defined in the Materials and Methods. GO terms/IDs and selected genes represent the top ontology from each cluster. Enrichment scores and P-values represent the entire cluster.