Integrative analysis identifies primary JunD targets in basal and LPS stimulated BMDMs.Jund gene expression patterns in WKY and WKY.LCrgn2 BMDMs over the LPS time course were used for Spearman correlation analysis with the rest of the transcripts on the microarrays (P < 0.001 cut off). The correlated genes were used for building the JunD target gene networks and selected based on i. significant differential expression following Jund siRNA knockdown (both basal and after LPS stimulation FDR< 5%), ii. presence of the JunD ChIP-Seq peak in WKY BMDMs (both basal and after LPS stimulation). The outer ring represents all the transcripts correlating with Jund expression levels (P<0.001) in WKY and WKY.LCrgn2 BMDMs (1445 transcripts, 75%, indicated in grey circles) over the LPS time course. Transcripts associated with a JunD ChIP-Seq peak (within 20kb of TSS or within the gene body) are shown as black circles (232 transcripts, 12%). The transcripts correlating with Jund expression levels and down-regulated following Jund siRNA (basal, upper panel) are shown in blue (125 transcripts, 6.5%); and those up-regulated (basal, upper panel) are shown as red circles (116 transcripts, 6%). Primary JunD targets in basal BMDMs are given with the gene names and show a JunD ChIP-Seq peak (24 transcripts, basal state, upper panel). This analysis was repeated for the LPS-stimulated macrophages taking into account JunD siRNA and ChIP-Seq datasets in LPS stimulated macrophages and identified 36 primary Jund targets (lower panel).
Hull et al. BMC Genomics 2013 14:92 doi:10.1186/1471-2164-14-92