Fig. 3

Association between histone modification differential enrichment and changes in gene expression. a Heatmaps showing clusters of genes (− 2 Kb) grouped by unique histone modification profiles identified in the soft clustering analysis (left) and corresponding changes in mRNA levels (right). ChIP-seq enrichment at the promoters and gene bodies is normalized (RPKM) and input-corrected. The signal corresponds to the ratio of ChIP-seq and mRNA levels in the infected versus the control condition. Data are log2-scaled and mean-centered. Representative profiles for each cluster showing various combinations of histone modification enrichment are included. All the profiles resulting from the soft clustering analysis are shown in Additional file 4: Figure S5. b Ratio of gene expression and histone modification enrichment between infected and control conditions for Mfuzz clusters more highly expressed in infected (left) and control (right) conditions. Data are the log2-scaled ratio between the infected and the control as in a. Spearman rank correlation coefficient (rho) and corresponding P value are shown for significant associations between histone modification enrichment and mRNA levels. c Histone enrichment profiles in the region containing the AGAP009887-encoding gene. Tracks show normalized/input-corrected ChIP-seq signals and RNA-seq mapped reads counts for each condition. The location of diffReps regions, MACS2 peaks, predicted transcription factor binding sites and predicted chromatin states for infected and control conditions are included. All tracks are shown at equal scale