Table 3.
Most enriched pathways.
| Pathway | Name | Source | pValue | Bonferroni | Genes from Input | Genes in Annotation |
|---|---|---|---|---|---|---|
| M5889 | Ensemble of genes encoding extracellular matrix and extracellular matrix-associated proteins | MSigDB C2 BIOCARTA (v7.3) | 6.717E-135 | 6.153E-132 | 140 | 1026 |
| M5884 | Ensemble of genes encoding core extracellular matrix including ECM glycoproteins, collagens and proteoglycans | MSigDB C2 BIOCARTA (v7.3) | 1.567E-85 | 1.435E-82 | 75 | 275 |
| 1270244 | Extracellular matrix organization | BioSystems: REACTOME | 2.416E-69 | 2.213E-66 | 67 | 298 |
| M3008 | Genes encoding structural ECM glycoproteins | MSigDB C2 BIOCARTA (v7.3) | 1.949E-55 | 1.785E-52 | 51 | 196 |
| M5885 | Ensemble of genes encoding ECM-associated proteins including ECM-affiliated proteins, ECM regulators and secreted factors | MSigDB C2 BIOCARTA (v7.3) | 1.738E-39 | 1.592E-36 | 65 | 751 |
| M3468 | Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix | MSigDB C2 BIOCARTA (v7.3) | 9.420E-30 | 8.629E-27 | 36 | 238 |
| 1270245 | Collagen formation | BioSystems: REACTOME | 5.373E-29 | 4.921E-26 | 26 | 93 |
| M18 | Beta1 integrin cell surface interactions | MSigDB C2 BIOCARTA (v7.3) | 2.802E-28 | 2.566E-25 | 23 | 66 |
| M7098 | ECM-receptor interaction | MSigDB C2 BIOCARTA (v7.3) | 5.997E-24 | 5.493E-21 | 22 | 84 |
| 1270256 | ECM proteoglycans | BioSystems: REACTOME | 4.440E-23 | 4.067E-20 | 19 | 57 |
Selection based on p-value and adjusted with Bonferroni correction. Hit count in genome shows the number of genes in a given pathway, and the hit count in query list shows how many genes in the query list are hit in a given pathway. The full output table generated by ToppFun is shown in Supplementary Table S4.