Table 6. Characterization of time- and virus-specific subnetworks.
| Cluster | Timing | In-cluster viruses | Out-of-cluster viruses | Enriched pathways | Enriched regulators |
|---|---|---|---|---|---|
| A | Sustained | H1N1 CA04 and NL; H5N1 NS1trunc | H5N1 WT, PB1-F2del, PB2-627E | JAK-STAT signaling*, antiviral and interferon response, many immune-response pathways, cell cycle | FOSL1, IRF7, ISG15p, LMO2, MAFF, MLKL, NFS1p, NMI, NUPR1, SP110, SSTR2, STAT1, TRIM21, TRIM5 |
| B | Sustained | H1N1 CA04 and NL; H5N1 WT, PB1-F2del, PB2-627E | NS1trunc | GPCR signaling | SAG, YTHDC1 |
| C | Sustained | H5N1 WT, PB1-F2del, PB2-627E | H1N1 CA04 and NL; H5N1 NS1trunc | Muscle contraction | DDR2, HCLS1, HOXA7, SAG, TAL2, YTHDC1 |
| D | Mid-late | H5N1 WT, NS1trunc, PB1-F2del, PB2-627E | H1N1 CA04 and NL | PPARA*, SCF KIT*, NFG*, FGFR* mutant signaling pathways | CCRN4L, CDKL2, CDKL3, CITED2, ETV3, MXD1, NR4A2, PAPOLG, PPP1R10, SNAI1, TCEB1, TOB1, WNK4 |
| E | Very late | H5N1 WT, NS1trunc, PB1-F2del, PB2-627E | H1N1 CA04 and NL | Circadian clock, Wnt signaling | ACVR1B, ERCC2, FBXL19, FOXH1, NKX2-5, PPP1R11, SAP30BP, TLX2 |
"Timing" describes the general timing under which the cluster is active; a value of 'sustained means that the cluster appears active throughout every time course. "In-cluster" lists the viruses represented in the cluster. 'Out-of-cluster' lists the viruses mostly absent from the cluster. "Enriched pathways" lists major enriched pathway terms
* indicates that the pathway was enriched only among regulators of the cluster network. "Enriched regulators" are the subset of cluster regulators for which their targets are statistically enriched in the cluster relative to all clusters.