Fig 6

(A) Gene co-expression network visualisation. Each node represents one gene, with node size proportional to the number of connected nodes (co-expressed genes). Edges represent co-expression between two genes, with edge weight proportional to the strength of co-expression. The co-expression network is a signed adjacency matrix constructed from RNA-seq data from wild type and heterozygous mutant zebrafish brains at 6 and 24 months of age. Only nodes with at least four connections are shown. Gene "modules" are groups of genes with similar expression patterns across heterozygous mutant and wild type zebrafish brains. In this network, 30 gene modules were identified using a hierarchical clustering and branch cutting method. Modules showing no significant changes in expression are coloured grey, modules showing significantly increased expression during wild-type brain aging are coloured red, while modules showing significantly decreased expression during wild-type brain aging are coloured blue. Modules with other colours also show signficantly altered expression during heterozygous mutant brain aging. See B for details. Asterisks indicate zebrafish brain gene modules which are significantly preserved in a co-expression network constructed from an independent human brain dataset. (B) Gene expression patterns of modules in the gene co-expression network across heterozygous mutant and wild type zebrafish brains at 6 months and 24 months of age. Values shown in cells are hybrid Pearson-robust correlations between the overall gene expression in a module (summarised using the first principal component) and experimental condition encoded as a binary variable (6-month-old heterozygous mutant, 24-month-old heterozygous mutant, 6-month-old wild type, 24-month-old wild type). Values in parentheses are unadjusted Student correlation p-values. Modules showing potentially altered expression patterns during heterozygous mutant aging compared to wild-type aging are labelled with coloured text, with colours corresponding to module colours in (A). Asterisks indicate zebrafish brain gene modules which are significantly preserved in a co-expression network constructed from an independent human brain dataset.