Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism
Fig 2
Transcription factor (TF) enrichment analysis.
(A) Total mRNAs identified in the endothelial cells and the numbers upregulated and downregulated following infection with KSHV using a negative binomial distribution with an FDR% of 1 (B.) Schematic of RNAseq and TF enrichment analysis. Three biological replicates of KSHV infected endothelial cells harvested at 48 hpi for RNAseq of mRNA were analyzed. TF-specific binding motifs identified upstream of transcription start sites and differential expression p-values between mock and KSHV-infected cells from RNASeq data were used for the motif enrichment hypothesis tests. Colored arrows represent transcription start sites. Red and blue lines represent downregulated and upregulated transcripts, respectively. Triangles represent transcription factors binding upstream of transcription start site. (C.) List of significant TFs that are predicted to be altered by KSHV during latency with a p < .05 that were used for the Steiner forest analysis.