Functional annotation of differentially expressed gene groups
| Gene cluster . | 6 h . | 24 h . | 48 h . | |||
|---|---|---|---|---|---|---|
| Viable . | AT2 . | Viable . | AT2 . | Viable . | AT2 . | |
| Up-regulated gene clusters | ||||||
| Endosome | 2.3 | 2.0 | ||||
| GTPase activity | 1.6 | 1.6 | 1.1 | |||
| Immune response | 1.4 | 1.1 | 5.2 | 7.6 | ||
| Induction of apoptosis/apoptosis | 1.0 | 1.0 | 1.6 | 2.3 | 1.4 | |
| NF-kB associated | 1.6 | 1.7 | 1.3 | |||
| TNFR2 signaling | 1.6 | |||||
| TNF/stress signaling | 1.6 | 1.3 | ||||
| MAPK signaling | 1.6 | 1.3 | ||||
| TLR signaling | 1.6 | 1.3 | ||||
| Translation/ribosomal parts | 1.5 | |||||
| Antiapoptosis | 1.5 | 1.4 | ||||
| Response to virus | 3.7 | 4.0 | ||||
| Down-regulated gene clusters | ||||||
| Mitochondria/respiration | 2.0 | 1.6 | 1.1 | 3.2 | 2.5 | |
| Nucleus associated | 1.7 | 1.6 | 1.1 | 2.3 | ||
| RNA splicing | 1.4 | 1.6 | 1.2 | 2.3 | ||
| Translation/ribosomal parts | 3.2 | 2.9 | ||||
| Lysosome | 2.7 | |||||
| Gene cluster . | 6 h . | 24 h . | 48 h . | |||
|---|---|---|---|---|---|---|
| Viable . | AT2 . | Viable . | AT2 . | Viable . | AT2 . | |
| Up-regulated gene clusters | ||||||
| Endosome | 2.3 | 2.0 | ||||
| GTPase activity | 1.6 | 1.6 | 1.1 | |||
| Immune response | 1.4 | 1.1 | 5.2 | 7.6 | ||
| Induction of apoptosis/apoptosis | 1.0 | 1.0 | 1.6 | 2.3 | 1.4 | |
| NF-kB associated | 1.6 | 1.7 | 1.3 | |||
| TNFR2 signaling | 1.6 | |||||
| TNF/stress signaling | 1.6 | 1.3 | ||||
| MAPK signaling | 1.6 | 1.3 | ||||
| TLR signaling | 1.6 | 1.3 | ||||
| Translation/ribosomal parts | 1.5 | |||||
| Antiapoptosis | 1.5 | 1.4 | ||||
| Response to virus | 3.7 | 4.0 | ||||
| Down-regulated gene clusters | ||||||
| Mitochondria/respiration | 2.0 | 1.6 | 1.1 | 3.2 | 2.5 | |
| Nucleus associated | 1.7 | 1.6 | 1.1 | 2.3 | ||
| RNA splicing | 1.4 | 1.6 | 1.2 | 2.3 | ||
| Translation/ribosomal parts | 3.2 | 2.9 | ||||
| Lysosome | 2.7 | |||||
Differentially expressed gene lists were generated for viable HIV-1–treated cells at 6, 24, and 48 hours using a B-value cutoff of −0.5 and for AT-2–inactivated cells using a B-value cutoff of −2.6. Separate lists were made for up and down-regulated genes. The web-based DAVID functional annotation software34 was used to group the genes according to their function, and the degree to which their expression was enriched (overrepresented) against the background of all the genes spotted on the arrays was determined. The numbers refer to the DAVID-generated enrichment factor. Numbers are shown only for those gene groups with an enrichment score greater than 1.