Fig. 6

Genome-wide transcriptional responses to acute starvation in wild-type P. pacificus. (A) Hierarchically clustered heat map showing the 1,007 genes that were identified as differentially expressed in response to 24 h of acute starvation (SRGs). Trees on the left and the top show clustering results based on similarity in expression levels. Numbers on the gene tree indicate the number of genes in each of the two response clusters. WT = wild type. (B) Bar chart showing the overrepresented gene-age classes and co-expression networks (according to [40]) identified the two response clusters, relative to the genome. “Phylogenetically old genes” refers to those genes in the genome of P. pacificus that are not diplogastrid-specific orphan genes. (C) Lollipop plot showing overrepresented PFAM domains in each response cluster. Y-axis gives PFAM domain names. X-axis gives the percentage of all unique genes encoding this PFAM domain, which were found to be present in the response cluster (e.g., 60% means that 60% all unique genes in the genome that encode this domain are present in that cluster). (D) Bubble chart showing overrepresented WormCat terms in each of the response clusters. Enriched functional categories were broken down into three hierarchical levels of increasing specificity (see WormCat legend in the upper right). Bold black fonts indicate terms of the highest functional level (i.e., category level 1) which represent different biological functions in the broadest sense. Non-bold black fonts indicate terms of the second category level (i.e., a more specific aspect of the overarching functional level). Gray italicized fonts indicate the most specific (and least inclusive) functional terms within the overarching categories for which an overrepresentation signal could be detected. Bubble size scales with the gene count indicated to the right of the bubble. The significance scale (q-value) depicted in (C) also applies to the bubbles depicted in (D)