ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature
Fig 6
ENQUIRE-generated graphs enhance the context resolution of pathway enrichment analyses.
A: reference dendrogram showcasing the expected categorization of the case studies described in Table 6. The number following a case study abbreviated name indicates the expansion counter. Network expansions that did not yield any new gene were excluded. B: Topology-based pathway enrichment, obtained by applying Q score propagation and SANTA’s KNet function on ENQUIRE-informed gene-gene associations (see Post Hoc Analyses under Materials and methods). The heatmap shows the unadjusted p-values for the 50 enriched Reactome pathways with at least one significant, adjusted p-value (5% FDR) and highest variance across case studies (the dendrogram was computed on the complete statistic). Pathways are clustered according to Reactome’s internal hierarchy. We respectively apportioned the dendrograms into 5 and 15 partitions to visualize their respective coherence to Major Topic and Reactome Categories. Legends for expansions, rounded corpus size, and p-values ranges are provided. C: Permutation tests of Baker’s gamma correlation between the reference dendrogram (A) and clustering obtained from alternative pathway enrichment analyses, as in B. Colored areas indicated probability intervals obtained from simulating correlations between reference and sampled dendrograms. See Materials and methods for further details.