Table 4.
Top functional categories enriched (> 5 genes, FDR-adjusted P-value < 0.05 and ≤ 5 molecular functions) among the genes coding for differentially abundant proteins in the WT_BCG versus WT_Sal, WT_BCG versus KO_BCG, and KO_BCG versus WT_Sal contrasts.
| Contrast and Categorya | GO Term or KEGG Pathway Name | Gene Count | FDR P-value |
|---|---|---|---|
| WT_BCG -WT_Sal | |||
| MF GO:0005198 | Structural molecule activity | 10 | 1.1E-04 |
| KEGG 05322 | Systemic lupus erythematosus | 9 | 1.1E-10 |
| KEGG 05034 | Alcoholism | 8 | 1.1E-07 |
| KEGG 05203 | Viral carcinogenesis | 5 | 6.9E-03 |
| PFAM PF00125 | Core histone H2A/H2B/H3/H4 | 15 | 4.4E-24 |
| WT_BCG-KO_BCG | |||
| BP GO:0006457 | Protein folding | 7 | 7.1E-03 |
| MF GO:0003676 | Nucleic acid binding | 31 | 5.5E-07 |
| MF GO:0097159 | Organic cyclic compound binding | 39 | 5.5E-07 |
| MF GO:1901363 | Heterocyclic compound binding | 39 | 5.5E-07 |
| MF GO:0003723 | RNA binding | 20 | 6.6E-06 |
| MF GO:0019904 | Protein domain specific binding | 12 | 1.1E-05 |
| KEGG 05322 | Systemic lupus erythematosus | 10 | 9.4E-11 |
| KEGG 05034 | Alcoholism | 9 | 1.0E-07 |
| KEGG 05203 | Viral carcinogenesis | 7 | 3.2E-04 |
| KEGG 04145 | Phagosome | 6 | 9.5E-04 |
| KEGG 04141 | Protein processing in endoplasmic reticulum | 5 | 7.9E-03 |
| KEGG 04810 | Regulation of actin cytoskeleton | 5 | 1.8E-02 |
| PFAM PF00125 | Core histone H2A/H2B/H3/H4 | 13 | 3.3E-17 |
| KO_BCG-WT_Sal | |||
| BP GO:0071822 | protein complex subunit organization | 16 | 1.1E-02 |
| BP GO:0051258 | protein polymerization | 5 | 4.7E-02 |
| BP GO:0043933 | macromolecular complex subunit organization | 18 | 4.8E-02 |
| MF GO:0003723 | RNA binding | 23 | 1.7E-06 |
| MF GO:0005198 | Structural molecule activity | 14 | 1.7E-06 |
| MF GO:0044822 | Poly(A) RNA binding | 19 | 1.4E-05 |
| MF GO:0003676 | Nucleic acid binding | 30 | 1.7E-04 |
| MF GO:0019899 | Enzyme binding | 19 | 2.4E-04 |
| KEGG 05322 | Systemic lupus erythematosus | 9 | 1.8E-08 |
| KEGG 05034 | Alcoholism | 8 | 8.7E-06 |
| KEGG 04145 | Phagosome | 7 | 2.5E-04 |
| KEGG 04540 | Gap junction | 5 | 1.4E-03 |
| KEGG 04141 | Protein processing in endoplasmic reticulum | 5 | 1.8E-02 |
| KEGG 05203 | Viral carcinogenesis | 5 | 3.3E-02 |
| KEGG 04810 | Regulation of actin cytoskeleton | 5 | 3.8E-02 |
| PFAM PF00125 | Core histone H2A/H2B/H3/H4 | 10 | 1.1E-10 |
| PFAM PF00091 | Tubulin/FtsZ family, GTPase domain | 5 | 2.7E-06 |
| PFAM PF03953 | Tubulin C-terminal domain | 5 | 2.7E-06 |
a
Contrast: WT = wild type mice; KO = IDO1 KO mice; Sal = saline treatment; BCG = Bacillus Calmette–Guérin treatment. Categories: Gene Ontology (GO) biological process (BP) and molecular function (MF); KEGG pathway; and protein family PFAM.