Fig. 4

Reversal of latent HIV-1 model—SDREM analysis. Whole genome transcriptome data in ACH-2 cells at multiple time points were analyzed by SDREM for a, b SAHA; c, d Prostratin; e, f TNF-α. a, c, d represent the regulatory part of the model, where each path represents a collection of gene expression profiles; x-axis denotes the time points for each treatment when the gene expression was measured and the y-axis shows log₂ fold change in expression. TFs that are predicted to control the split are included at indicated time points (TFs are included only the first time they are active along a regulatory path). TFs in red or blue indicate that transcripts of these TFs were also observed to be significantly increased or decreased respectively. The size of the node indicates the relative number of genes regulated. b, d, f represent oriented interaction network starting from upstream proteins (source; red), predicted signaling proteins (blue) and active TFs (green). The boldness of the edge between two nodes, indicate the number of pathways between the two