Figure 3

Pair-wise similarity matrix of literature-defined pathways. The Jaccard index (a similarity metric) between all pairs of 128 pathways represented as a hierarchically clustered heatmap (A). For brevity, source databases are indicated by number: GeneGo [1] KEGG [2], NCI-PID [3], NetPATH [4], PANTHER [5], and Reactome [6]. The GeneGo database [1] sub-categorizes pathways based on the use of alternate downstream effectors, as indicated in the labels. 7 dense pathway clusters are highlighted via black circles and labelled I through VII. Focusing on 4 extensively studied pathways (EGF, TGF-β, TNF-α, and Wnt; B through E respectively), Jaccard index matrices for the same pathway as defined in different database sources. Note the high level of discordance between alternate sources.