We used TopHat [49] version 2.0.13 for aligning the Illumina short reads against the reference human genome (Grch38.p7 http://www.gencodegenes.org/releases/25.html) as well as a reference GTF file constructed from Illumina’s iGenome annotation archive (http://cufflinks.cbcb.umd.edu/igenomeshtml, Homo Sapiens NCBI Grch38.p7). RESM (RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome)and edgeR (edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.) were used to summarize the gene expression values as FPKM measures and to compare cell lines to identify genes with differential expression, separately. (Pvalue ≤ 0.05, FDR ≤ 0.001, fold change ≥2). Functional annotation for GO/KEGG was enriched by EnrichPipeline https://sourceforge.net/p/enrichmentpipeline/wiki/Home/STEM was used to do Time course cluster analysis (v1.3.9 STEM: a tool for the analysis of short time series gene expression data) Additionally, the results of gene expression (fold change and Pvalues) were overlaid with known protein-protein interactions33,34 in the Cytoscape35 software for network-based analysis and visualization.
