Fig. 4

Genomic concordance of MODifieR modules on MS use case data. (a) Heatmap of PASCAL P-values for eight single-method MODifieR modules, identified for 11 MS-related transcriptomic datasets. Module performance P-values are shown in a white to blue scale, where any shade of blue represents a significant module (P < 0.05), white represents a non-significant module, and grey represents a module of size zero. Datasets are classified into the reported MS type: MS (blue), RRMS (red), PPMS (green), SPMS (orange), and CIS (yellow); and four cell types: whole blood (maroon), PBMCs (light brown), white matter (light yellow), and CD4+ T cells (purple). Datasets are meta-P-values of the single-method enrichments (dataset score, bottom boxplot). MODifieR methods are organized by algorithm type: seed-based (green), co-expression-based (yellow), and clique-based (red). Single methods are scored by P of the significant modules across datasets (method score, right boxplot). (b) Heatmap of PASCAL P-values for four single-method MODifieR modules, identified for nine MS-related transcriptomic datasets. (c-d) Bar plots of Pascal P-values for the MS consensus modules generated with Clique SuM from transcriptomic (a) and methylomic (b) datasets. (e) Union and intersection of the top performing modules, shown as a Venn diagram