Table 1.
VN1203 influenza host transcriptional modulesa
| Module | Module validationb (P value) | Total no. of transcripts | No. of DE transcripts | FC trend | No. of DE transcripts at 7 hpi | Representative GO functional enrichment (P value) |
|---|---|---|---|---|---|---|
| Blue | 0 | 2,283 | 1,910 (83.7%) | Up | 363 | Inflammatory response, chemotaxis response to wounding, response to virus |
| Green | 0 | 1,300 | 1,217 (93.6%) | Up | 5 | Ion transport, synaptic transmission, keratinization, immune system process |
| Black | 0 | 402 | 336 (83.6%) | Up | 1 | Negative regulation of transcription, chromatin modification, nonsense-mediated decay |
| Red | 0 | 901 | 649 (72%) | Up | 88 | NA |
| Pink | 0 | 397 | 315 (79.3%) | Up | 4 | Transcription, negative regulation of transcription |
| Grey 60 | 0 | 34 | 30 (88.2%) | Up | 0 | Response to stress, establishment and/or maintenance of chromatin architecture |
| Purple | 0 | 78 | 32 (41.0%) | Mixed | 4 | Cell cycle, transcription, RNA elongation |
| Salmon | 0 | 68 | 0 (0.0%) | Mixed | 0 | NA |
| Green-yellow | 0.004 | 75 | 0 (0.0%) | Mixed | 1 | NA |
| Light cyan | 0 | 49 | 12 (24.5%) | Mixed | 0 | Phosphate transport |
| Turquoise | 0 | 6,735 | 5,407 (80.3%) | Down | 103 | Regulation of Ras protein signal transduction, carbohydrate metabolic process, tRNA aminoacylation for protein translation, protein complex assembly, regulation of Rho protein signal transduction, protein transport, M phase of mitotic cell cycle |
| Cyan | 0 | 54 | 45 (83.3%) | Down | 1 | RNA splicing, regulation of apoptosis |
a
WGCNA-derived modules were assessed for differential expression, general trending, and contribution to the early response. DE, differential expression; FC, fold change; NA, not available (i.e., no functional categories were enriched).
b
A validation test was performed by comparing each module's average topological overlap (TO) similarity (i.e., the similarity in transcript expression patterns) to those of randomly sampled transcripts of the same group size. We also show representative Gene Ontology (GO) categories found to be enriched using hypergeometrics (FDR-adjusted P value, <0.05). See Table S2 in the supplemental material for all enriched GO categories and their corresponding P values.