Fig. 5

DMR genes were enriched for GO terms related to neural development and activity. a: Heatmap of pairwise Pearson correlations between GO terms (rows and columns) and dendrogram showing the results of unsupervised hierarchical clustering. Each GO term was represented by a vector of all DMR genes where values of 1 or 0 indicated the presence or absence, respectively, of a given gene in the term, then these vectors were used to compute correlations. Clusters of GO terms that shared many of the same DMR genes are denoted by black boxes. See Additional file 2: Table S5A for all DMR genes in each GO term. b: Names of enriched GO terms (rows), preceded by their significance rank, e.g. 1-synapse was the most significant. Different shades of blue to the left denote clusters and sub-clusters of GO terms, broadly defined as related to development (Dev) or activity (Act). The same color-cluster mappings are used in Fig. 6 and Additional file 1: Figure S10C and Figure S13. c: Heatmap of Pearson correlations between the first five principal components (PCs) of the correlation matrix in a (columns) and GO terms, represented by gene vectors as in a (rows). The name of each PC is followed in parentheses by the amount of variance it explained within the GO term correlations. Red and blue denote strong positive and negative correlations, respectively. Values are shown for correlations significant after Bonferroni correction for 215 tests (5 PCs × 43 GO terms). d: Bars plot -log10(Benjamini-Yekutieli-adjusted p-values) for each term. Vertical grey lines represent p-values of 0.05, 0.01, 1e-4. Bar color represents the average DMR log2(D/ND) methylation fold-difference for genes in the term, where darker red or blue represent higher mean methylation levels in D or ND fish, respectively. This quantity is referred to as log2fc in Additional file 1: Figure S2 and Additional file 2: Table S1