Table 4.
Gene sets associated with gene downregulation in gp120 + ddC using gene set enrichment analysis
| Gene set name | Top 5 genes | Source | Size | NOM p-val | FDR q-val |
|---|---|---|---|---|---|
| PROTEASOME_DEGRADATION | Psmc6, Rps27a, Psma4, Psma1, H2afz | Broad Institute | 39 | 0 | 2.40e−04 |
| PROTEASOME | Psma2, Psma4, Psma1, Psma5, Psmb1 | GenMAPP | 18 | 0 | 3.60e−04 |
| RIBOSOMAL_PROTEINS | Rps24, Rps27a, Rps25, Rpl21, Rpl7 | GenMAPP | 86 | 0 | 7.21e−04 |
| STRIATED_MUSCLE_CONTRACTION | Tpm1, Ttn, Tnnt1, Tnni1, Myl2 | GenMAPP | 39 | 0 | 0.003 |
| PROTEASOMEPATHWAY | Psma2, Psma4, Psma1, Psma5, Psmb1 | BioCarta | 22 | 0 | 0.02 |
| ELECTRON_TRANSPORT_CHAIN | Cox6a2, Cox17, Nduf5, Cox7b, Ndyfs4 | Broad Institute | 80 | 0 | 0.021 |
| ROME_INSULIN_2F_UP | Dpysl3, Ppp1r12a, Sh3glb1, Canx, Tpm1 | Rome et al., J. Biol. Chem., 2003 | 204 | 0 | 0.161 |
| DNA_REPLICATION_REACTOME | Orc3l, Prim2a, Rfc1, Rps27a, Orc4l | GenMAPP | 34 | 0.002 | 0.075 |
| OXIDATIVE_PHOSPHORYLATION | Cox6a2, Ndufa5, Cox7b, Atp6v1d, Atp5o | KEGG | 48 | 0.003 | 0.066 |
| RNA_TRANSCRIPTION_REACTOME | Ccnh, Gtf2f2, Cdk7, Mnat1, Polr2g | GenMAPP | 28 | 0.009 | 0.115 |
| PORPHYRIN_AND_CHLOROPHYLL_ METABOLISM | Eprs, Blvra, Cp, Urod, Hmox1 | GenMAPP | 18 | 0.020 | 0.153 |
| UBIQUITIN_MEDIATED_PROTEOLYSIS | Ube2b, Ube2n, Ube2g1, Ube2d3 | GenMAPP | 20 | 0.022 | 0.1813 |
Top 5 genes – top 5 ranking genes belonging to a gene set; source – source for the gene set; size – number of genes in a gene set; NOM p-val – nominal p value; FDR q-val – false discovery rate.