Network analysis in coordination with microarray data. Analysis combing the integrated Drosophila gene network and microarray data from Teleman et al. . (a) The network represents the differentially expressed genes in starved versus fed larval muscle tissue that could also be found in . Several examples of categories of genes listed in Teleman et al. are highlighted: cuticle, cellular respiration (Cell. Resp.), signal recognition particle (SRP), mitochondrial ribosomal proteins (mRP), ribosomal proteins (RP), and tRNA synthetases (Aats). The clustering of genes is a result of the integrated network and was done irrespective of the gene expression data from Teleman et al. (b) The subnetwork is the network built from a seeded set of SRP-related genes as defined by Teleman et al. and derived from (see Materials and methods section for seeded network construction). Gene expression ratios reflect wild-type larval muscle tissue upon starvation over wild-type larval muscle tissue under normal feeding conditions, where green represents genes down-regulated upon starvation and red genes up-regulated upon starvation. All nodes with a dark outline are differentially expressed (DE) genes as defined in Teleman et al. The diamond nodes are the seed genes, the circle nodes are genes reported as DE in Teleman et al. but not used as seed genes, and the hexagon nodes are genes not reported as DE by Teleman et al. The genes in the network in (b) were then treated as a gene set and used as input to GSEA . (c) The enrichment plot for all genes in the network in (b). Additionally, we performed an GSEA analysis on the genes in the network in (b) that did not include the seed genes (which corresponds to the set of genes that are circle and hexagon-shaped). (d) The enrichment plot for this set of genes showing that the network places together similarly regulated genes that are still significantly enriched even when the set of genes defined in Teleman et al. were excluded. See Figure S3 at  for more detail on the global performance of gene sets. The gene set representing (d) corresponds to the purple line in Figure S3a at .
Costello et al. Genome Biology 2009 10:R97 doi:10.1186/gb-2009-10-9-r97