Fig. 2

GeneWalk identifies myelination functions from mouse brain RNA-seq. a Schematic of the experimental design in Darbelli et al. [45]. Deletion of Qki, a gene that encodes RNA-binding proteins, in oligodendrocytes results in hypomyelination in the mouse brain. RNA-seq was performed on Qki-deficient and control mice (each three biological replicates). b Schematic with statistics of the qki GeneWalk networks (GWNs) using either INDRA or Pathway Commons (PC) as a knowledge base. Also shown is a visualization of the INDRA GWN subnetwork of myelination-related genes Mal, PllP, and Plp1, all their connected genes and GO terms. Edges (gray) connecting node pairs indicate the presence of INDRA reaction statements or GO annotations between the two respective nodes. Edges between Mal and its GO connections (numbered according to rank order in c) are highlighted (bold). c GeneWalk results for Mal in the qki condition using either INDRA or Pathway Commons (PC) as a knowledge base source to assemble the GeneWalk network. All GO terms connected to Mal are rank-ordered by Benjamini-Hochberg FDR-adjusted p-value (p-adjust), indicating their functional relevance to Mal in the context of Qki deletion in oligodendrocytes. Error bars indicate 95% confidence intervals of gene p-adjust. FDR = 0.1 (dashed red line) and domains of GO annotations (square: biological process, triangle: cellular component, and circle: molecular function) are also shown. Additional file 1 shows full GeneWalk results using the INDRA or PC knowledge base. d As in c for Plp1