Figure 2.

RNA sequencing (RNA-seq) analysis results and function enrichment analysis of differentially expressed genes. (A) Unsupervised hierarchical cluster analysis of 401 differentially expressed genes in the pair-wise comparisons. There are 4 samples in each group. Pseudocolors indicate differential expression (red, up-regulation; green, down-regulation; black, no change in expression). (B) Venn diagram of differentially expressed genes in PBMC samples following PPD stimulation with P < 0.05 by Students' t-test and ratio >2.0. (C) Regulatory network built from the differentially expressed genes between ATB and LTBI group. Circle nodes represents genes, while Gray filled rectangle nodes with yellow border color indicate biological processes. For genes, borders of the nodes represent the type of the gene (up regulated in red, down regulated in green), centers of the nodes indicate the gene expression changes, color intensity is proportional to the level of regulation. Genes that not quantified are shown in gray. Protein-protein interactions are depicted as gray solid line, dashed lines show the linkage of gene to related biological processes. Big gray circles indicate main module of biological processes. (D) Gene Ontology (GO) enrichment analysis for differentially regulated genes between ATB and LTBI group. Only the top false discovery rate (FDR) ranked 10 enrichment of GO terms from “biological process” category were listed.