Fig. 2

Network enrichment of experimentally perturbed genes. The summary of gene set (DEG vs. pathways or TFs) connections in the global network was performed using NEA. For description of the computational procedure see “Network enrichment analysis” in Methods. Lists of DE genes characterized either 1) expression change in the course of confrontation with tumor cells or 2) differential inhibition capacity of fibroblasts in regard of tumor cells. Red: lists of differentially expressed genes (DEG) from our experiment. Green: annotated pathways from public resources enriched in connections to DEGs. Yellow: individual transcription factors (TF) selected for their enrichment in network connections to DEGs. Lines are NEA-based summaries of individual, gene-gene network edges that connect DEGs and pathways between which significant network enrichment was detected (minimal NEA FDR < 0.01 and number of individual gene-gene links (see edge labels) at least 10 per pathway and at least 3 per TF). The image was created using software Cytoscape [39]