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Fig. 4 | Genome Biology

Fig. 4

From: Extensive rewiring of epithelial-stromal co-expression networks in breast cancer

Fig. 4

Comparative functional network enrichment analysis on the normal breast, ER-positive IBC, and ER-negative IBC epithelial-stromal co-expression networks. a–c Scatterplots where each point is a functional geneset plotted according to its statistical significance in two of the epithelial-stromal co-expression networks. The terms are colored according to the category of geneset, with black indicating a breast cancer prognostic geneset; blue indicating a KEGG biological pathway; green indicating a GO biological process; and red indicating a cell type-specific signature. A subset of top-ranking genesets is labeled in the plots. In a, each geneset is plotted according to its statistical significance in the ER-positive IBC network on the y-axis and the normal network on the x-axis. In b, each geneset is plotted according to its statistical significance in the ER-negative IBC network on the y-axis and the normal network on the x-axis. In c, each geneset is plotted according to its statistical significance in the ER-negative IBC network on the y-axis and the ER-positive IBC network on the x-axis. d Venn diagram depicting genesets identified as significantly enriched (FDR < 5 %) in at least one of the three networks. ER estrogen receptor; ES epithelial-stromal; GO Gene Ontology; IBC invasive breast cancer; KEGG Kyoto Encyclopedia of Genes and Genomes; Neg negative; Norm normal; Pos positive

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