ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature
Fig 3
Example of ENQUIRE’s post hoc analyses.
We used the PubMed identifiers (PMIDs) generated by the query (“Ferroptosis”[MeSH terms] AND “Immune System”[MeSH terms]) NOT “review”[Publication Type] as input and obtained ENQUIRE-reconstructed gene and MeSH co-occurrence networks. A: output of the automatic gene set reconstruction, using the original gene/MeSH network as input and fuzzy c-means. Nodes referring to genes are labelled, and those belonging to clusters containing 2 or more genes are represented as pie charts. Sector sizes of the pie-chart-shaped nodes reflect their relative membership degree to each gene set cluster. For simplicity, a color legend and description are provided only for gene sets of size 3 or bigger. B: topology-based enrichment analysis of Reactome pathways, using original and expanded networks, as described in Materials and methods. 30 pathways whose FDR-adjusted p-value was significant in at least two networks are depicted. Reactome pathways are grouped based on “Top-Level Pathway” and “Disease” categories. Green and white-yellow-red gradients respectively indicate the expansion counter and observed, unadjusted p-values.