a-f. Transcriptional network clustering of expression data from RNAi treated BMDMs – median expression profiles. A network graph was clustered from microarray data using Pearson correlation r ≥ 0.9 & Markov clustering algorithm (MCL inflation value of 2.2). 4a: Five main clusters of co-expression emerged containing genes influenced most by siRNA & IFNγ treatment. A consistent disruption of transcriptional activity of BMDM was observed using six particular siRNAs (shaded in blue) targeting Ifnb1, Irf3, Irf5, Nfkb2, Stat1 & Stat2 mRNAs. 4b: Cluster 1 – 234 genes whose expression is induced by IFNγ and repressed by the six active siRNAs. 4c: Cluster 2 – 179 genes repressed by IFNγ but de-repressed by six siRNAs. 4d: Cluster 3 – 67 genes whose expression is not influenced by IFNγ at 24 hour assay point but repressed by six siRNAs. Many of these are innate immune response genes 4e: Cluster 4 – 86 genes de-repressed by siRNAs, many of which have known functional association with cell cycle 4f: Cluster 5 – 44 genes enriched with annotation for NF-kB signalling.
Lacaze et al. BMC Genomics 2009 10:372 doi:10.1186/1471-2164-10-372