Table 2 Annotation for co-expressed gene clusters derived from RNAi and IFNγ treatments.

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%