Fig. 3

Overlapping entities across modalities in the three databases studied (i.e., KEGG, Reactome, and WikiPathways). The comparison analysis studied the degree of overlap for three different biological entities (i.e., genes, metabolites, and miRNAs) to evaluate whether entities are shared across databases (i.e., the ratio of the number of nodes present in all three databases to the number of nodes in the union of all databases for that modality), partially overlap (i.e., the ratio of the number of nodes present in only two databases to the number of nodes in the union of all databases for that modality) or are exclusive (i.e., the ratio of the number of nodes unique in one database to the number of nodes in the union of all databases for that modality). The classification of entities by their corresponding modalities are described in Table 2. We would like to remark that the analysis accounted for every entity present in the full set of pathways from the studied databases