Modulated Modularity Clustering as an Exploratory Tool for Functional Genomic Inference
Panels (A)–(D) describe a systems genetic analysis of 414 Drosophila melanogaster genes associated with a competitive fitness phenotype. (A) The reordered matrix of pairwise genetic correlations between transcriptional profiles, in analogy to Figure 3F. The twenty clusters identified by MMC are numbered (Modules 1–20), color-coded (to the left and below), and emphasized with borders. From the upper left (Module 1) to lower right (Module 20), modules are ordered by decreasing average connectivity, defined here as average absolute pairwise correlation within the module. (B) Relevance network obtained from the 414 genes by enforcing an absolute correlation threshold of . The genes are numbered and color-coded as in (A) to indicate module membership. Only genes with at least one connection are shown. (C) Bar chart of the genes in Module 9 reporting for each one its relative expression level across eleven tissues. Genes are shown on the -axis, tissues are shown on the -axis, and relative expression is shown on the -axis. Expression in the ovary has been highlighted in red, and the genes featured in the next panel have been highlighted in blue. (D) Local alignment of five genes sharing the dsx motif in their 5′ UTRs. Above the alignment, a logo is shown to represent the profile of the 17 bp recognition sequence of doublesex.