Table 2

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

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%


*For full gene membership see Supplementarty table 2.

Lacaze et al. BMC Genomics 2009 10:372   doi:10.1186/1471-2164-10-372

Open Data