| Cluster 1 | Cluster 2 | Cluster 3 | Cluster 4 | Cluster 5 |
---|---|---|---|---|---|
Cluster designation | IFNγ induced genes | IFNγ repressed genes | IFNβ induced genes | Cell cycle regulators | NFkB signalling genes |
No. genes in cluster (Pearson r = 0.9) | 234 | 179 | 67 | 86 | 44 |
IFNγ treatment effect (at 24 hr assay point) | Up-regulation | Repression | No effect | No significant effect | No significant effect |
siRNA effect (Ifnb1, Irf3/5, Stat1/2, Nfkb2) | Repression | Up-regulation (De-represssion) | Repression | Up-regulation (De-reprsssion) | Repression |
Representative GO Terms (p < 0.05) | Immune response, Antigen presentation | Intracellular signalling, Negative regulation of cellular process | Innate immune response, Inflammatory response | Cell cycle, DNA metablism, DNA replication | Stess response, Inflammatory response |
Enriched KEGG pathways (p < 0.05) | TLR signalling, Cytokine-cytokine receptor, Cell adhesion molecules, JAK-STAT signalling | - | TLR signalling, Cytokine-cytokine receptor interaction | Cell cycle, DNA polymerase, Pyrimidine/purine metabolism | MAPK signalling, Apoptosis |
Promoter analysis (p < 0.05) | ISRE sequence (34/234) NFkB targets (14/234) | - | ISRE sequence (16/67) | - | NFkB targets (12/44) CREB targets (4/44) |
Representative gene membership* | Ccl2, Cxcl9, Cxcl11, Vegfa, Il15, Il18, Irf1, Irf2, Irf5, Ciita, Stat1, Stat3, Gbp1–5, Cd86, Itgb7, Cd274, Tlr6, Tlr9, Nod1, H2-Aa/H2-Ab1/Dmb2/Ea | Cd28, Cd33, Cd5l, Cdk6, Cebpa, Socs6, Igf2, Pfcd4, Dusp7 | Isg20, Ifit1, Ifit2, Ifih1, Oasl1, Oas3, Mx1/2, Myd88, Tlr3, Ccl5, Ccl7, Ccl12, Stat2, Tnfrsf1a | Ccne1/2 Ccna2, Cdc2a, Cdca5, Cdca8, Cdc45l, Chek1, Brca1, Mcm2/3/4/5/6/7/10 Pola1, Pold1/e/e2 | Nfkb1/2, Nfkbia/z, Ikb, Il1a/b, Tnf, Cxcl1/2, Nos2, Socs3, Tnfaip2/3 |
Genes regulated by Lipofectamine2000 & non-specific siRNA transfection | 52/234 22.2% | 10/179 5.6% | 46/67 68.7% | 69/86 80.2% | 10/44 22.7% |