TABLE 5.
Functional enrichment analysis of genes identified as being coexpressed by WGCNA
| Gene module | No. of probes | Representative enriched gene functiona (enrichment score) | ISG content (%)b |
|---|---|---|---|
| M1 | 1,140 | Microtubule-based process (10), cell projection assembly (10) | 6.0 |
| M2 | 922 | Immune response (10), innate immune response (10), adaptive immune response (10), inflammatory response (10), cytokine production (10), lymphocyte activation (10), lymphocyte migration (10), positive regulation of apoptotic process (10), coagulation (10), hemopoiesis (10), homeostatic process (10), IFN-γ production (3.7) | 18.4 |
| M3 | 859 | Antigen processing and presentation of peptide antigen via MHC class I (10), macromolecular complex subunit organization (10), intracellular protein transport (10), RNA catabolic process (10), translation (10), viral infectious cycle (10), G1/S transition checkpoint (10), regulation of apoptotic process (2.6) | 8.1 |
| M4 | 858 | – | 3.3 |
| M5 | 377 | – | 4.2 |
| M6 | 291 | Immune response (10), innate immune response (10), cytoplasmic pattern recognition receptor signaling pathway in response to virus (10), type I interferon production (10), type I interferon-mediated signaling pathway (10), response to virus (10), cytokine production (10), cytokine-mediated signaling pathway (10), I-κB kinase/NF-κB cascade (10), regulation of apoptotic process (10), IFN-γ-mediated signaling pathway (5.8), RIG-I signaling pathway (3.4), JAK-STAT cascade (2.8), ISG15-protein conjugation (2.5) | 62.9 |
| M7 | 138 | Immune response (10), innate immune response (5.1), pattern recognition receptor signaling pathway (3.4), cytokine-mediated signaling pathway (3.3), regulation of sequence-specific DNA binding transcription factor activity (3.0) | 36.2 |
| M8 | 133 | Microtubule-based process (10), mitosis (10), mitotic cell cycle (10) | 6.8 |
| M9 | 128 | Antigen processing and presentation of peptide antigen via MHC class I (10) | 35.9 |
| M10 | 75 | – | 26.7 |
| M11 | 38 | Neurotransmitter receptor activity (GO molecular function) (2.7), cation transmembrane transporter activity (GO molecular function) (2.6) | 2.6 |
a
Genes in each module were analyzed using ToppCluster to identify enriched GO biological processes and GO molecular functions. ToppCluster used the Fisher exact test for enrichment and reports an “enrichment score” that is the −log10 of the BH-adjusted P value. Because many GO annotations are related, representative terms were selected to summarize the enrichment results. M11 was not enriched by any GO biological process but was enriched by GO molecular functions. –, No enriched GO function was identified.
b
The ISGs in each module were identified by using Interferome.