Fig. 3

Analysis of whole genome transcriptome data. a Time kinetics of whole genome transcriptome analysis in ACH-2 cells treated with SAHA, prostratin and TNF- α. Genome Studio was used to analyze transcriptome data obtained from Illumina HT-12 V4 array bead chips for ACH-2 cells treated with different reactivating agents at indicated time points. A differential score of ±13 (dotted line) corresponding to a p < 0.05 was used to identify the significant genes. Each data point corresponds to a differential score of an individual transcript calculated from results obtained in two independent experiments. b Dysregulated genes (p-value <0.05 and fold change ±2) from GenomeStudio transcriptome analysis were analyzed using MSigDB version 4.0 (http://www.broadinstitute.org/gsea/msigdb/annotate.jsp). The stacked bar graph represents the number of genes in each functional category for different time points in ACH-2 cells treated with SAHA, prostratin or TNF-α