ENQUIRE automatically reconstructs, expands, and drives enrichment analysis of gene and Mesh co-occurrence networks from context-specific biomedical literature
Fig 5
Protein-coding genes from ENQUIRE-generated graphs significantly share functional associations.
Panels A and B respectively report the unadjusted p-value density distributions of STRING-informed edge counts and DeltaCon similarities, arranged by number of protein-coding genes (network size). We used the H. sapiens functional association network from STRING to evaluate ENQUIRE-derived networks of protein-coding genes. We tested 733 networks having 10 or more possible network realizations given the observed degree sequence. For each observed network size and degree sequence of ENQUIRE-generated gene networks, 1,000,000 and 10,000 samples were respectively generated to perform a test statistic on the observed edge counts and DeltaCon similarities. See Materials and methods for additional information. The 733 tested networks are apportioned into quartiles based on network size, and for each the exact size is indicated (n). Within each network size interval, grey and red areas respectively highlight insignificant and significant p-values with respect to a globally-applied Benjamini-Hochberg correction (BH), and a percentage is indicated for those below 1% FDR. Diamonds indicate the observed data.