Figure 3
A more deviated transcriptome in Attacker virgin males. (A) RRHO analysis of all expressed genes in the “Attacker” vs “Parental” and “Attacker” vs “Father” comparisons, demonstrating either a discordant (top left and bottom right quadrants), or a concordant relationship (top right and bottom left quadrants). The overlap is made in a whole-transcriptome and threshold-free manner, where each pixel represents an overlap of the ranked lists. The color of each pixel represents the Benjamini–Yekutieli adjusted − log10(p value) of a hypergeometric test, with warmer colors reflecting more significance. (B) Clustered heatmap of all differential genes in each of the four comparisons. The analysis was done by the “pheatmap” software, with rows representing z-scores of normalized gene expression among the four groups in the analysis. The eight clusters (I–VIII) were generated using k-means clustering based on the normalized z-score of genes. (C) GOMCL cluster analysis of genes in heatmap cluster VI (B). Significantly over-represented biological process gene ontologies were represented in 10 clusters with reduced redundancy. The chart describes the ten simplified clustered pathways with the respective number of pathways included and the number of unique genes within each pathway to the right. Representative GO Biological Process Pathways of GOMCL cluster 1 and cluster 2 are displayed in (D,E), respectively. The over-represented pathways were modeled using the hypergeometric test with the whole annotated transcriptome as background. The color gradient of each bar represents the enrichment ratio (observed/expected), with brighter color showing higher enrichment. The x-axis represents − log10 transformed FDR values.
