Fig. 3

Correcting for gene overlap results in a sparser pathway co-occurrence network. a The KEGG pathway annotations for the sulfonate transport system are a subset of those for sulfur metabolism. 12 genes annotated to the sulfonate transport system are also annotated to sulfur metabolism. b Without applying the overlap correction procedure, 25 of the genes in the positive and negative gene signatures of the eADAGE feature “Node 11” are annotated to sulfur metabolism—of those, 8 genes are annotated to the sulfonate transport system as well. c All 8 of the overlapping genes are mapped to the sulfur metabolism pathway after overlap correction. d A co-occurrence network built without applying the overlap correction procedure will report co-occurrence between the sulfonate transport system and sulfur metabolism, whereas (e) no such relation is identified after overlap correction.