Table 1.
Functional pathway enrichment analysis of significantly upregulated and downregulated genes in Combination exposed vs Control group.
| Category | Term | Count | p-value | FE | Bonferroni | Benjamini | FDR | ||
|---|---|---|---|---|---|---|---|---|---|
| Upregulated | |||||||||
| Annotation Cluster 1 | REACTOME_PATHWAY | R-RNO-5389840: Mitochondrial translation elongation | 6 | <0.001* | 8.89 | 0.05 | 0.05 | 0.54 | |
| (2.371) | REACTOME_PATHWAY | R-RNO-5419276: Mitochondrial translation termination | 6 | <0.001* | 8.66 | 0.05 | 0.03 | 0.61 | |
| UP_KEYWORDS | Ribosomal protein | 5 | 0.021* | 4.70 | 0.96 | 0.36 | 22.60 | ||
| UP_KEYWORDS | Ribonucleoprotein | 5 | 0.057 | 3.42 | 1.00 | 0.61 | 50.38 | ||
| Annotation Cluster 2 | GOTERM_CC_DIRECT | GO:0016021, integral component of membrane | 17 | 0.999 | 0.52 | 1.00 | 1.00 | 100.00 | |
| (2.182) | UP_KEYWORDS | Transmembrane helix | 19 | 0.999 | 0.53 | 1.00 | 1.00 | 100.00 | |
| UP_KEYWORDS | Transmembrane | 19 | 0.999 | 0.53 | 1.00 | 1.00 | 100.00 | ||
| UP_KEYWORDS | Membrane | 24 | 0.999 | 0.56 | 1.00 | 1.00 | 100.00 | ||
| Downregulated | |||||||||
| Annotation Cluster 1 | INTERPRO | IPR015880:Zinc finger, C2H2-like | 5 | 0.076 | 3.08 | 1.00 | 1.00 | 64.49 | |
| (0.982) | INTERPRO | IPR007087:Zinc finger, C2H2 | 5 | 0.093 | 2.86 | 1.00 | 1.00 | 71.40 | |
| SMART | SM00355:ZnF_C2H2 | 5 | 0.160 | 2.31 | 1.00 | 1.00 | 83.54 | ||
| Annotation Cluster 2 | UP_KEYWORDS | Membrane | 30 | 0.195 | 1.18 | 1.00 | 1.00 | 91.64 | |
| (0.633) | UP_KEYWORDS | Transmembrane helix | 25 | 0.251 | 1.17 | 1.00 | 1.00 | 96.35 | |
| UP_KEYWORDS | Transmembrane | 25 | 0.259 | 1.17 | 1.00 | 0.99 | 96.78 | ||
| Annotation Cluster 3 | INTERPRO | IPR007110:Immunoglobulin-like domain | 4 | 0.251 | 2.27 | 1.00 | 1.00 | 97.48 | |
| (0.435) | INTERPRO | IPR003599:Immunoglobulin subtype | 3 | 0.378 | 2.26 | 1.00 | 1.00 | 99.77 | |
| SMART | SM00409:IG | 3 | 0.522 | 1.69 | 1.00 | 1.00 | 99.95 | ||
| Annotation Cluster 4 | INTERPRO | IPR000719:Protein kinase, catalytic domain | 4 | 0.279 | 2.14 | 1.00 | 1.00 | 98.47 | |
| (0.403) | INTERPRO | IPR011009:Protein kinase-like domain | 4 | 0.322 | 1.98 | 1.00 | 1.00 | 99.30 | |
| INTERPRO | IPR008271:Serine/threonine-protein kinase, active site | 3 | 0.332 | 2.50 | 1.00 | 1.00 | 99.42 | ||
| UP_KEYWORDS | Kinase | 4 | 0.393 | 1.75 | 1.00 | 0.99 | 99.68 | ||
| INTERPRO | IPR017441:Protein kinase, ATP binding site | 3 | 0.422 | 2.06 | 1.00 | 1.00 | 99.91 | ||
| SMART | SM00220:S_TKc | 3 | 0.551 | 1.61 | 1.00 | 1.00 | 99.97 | ||
| GOTERM_BP_DIRECT | GO:0006468~protein phosphorylation | 3 | 0.551 | 1.61 | 1.00 | 1.00 | 100.00 | ||
| Annotation Cluster 5 | GOTERM_MF_DIRECT | GO:0003682~chromatin binding | 4 | 0.208 | 2.50 | 1.00 | 1.00 | 94.18 | |
| (0.273) | UP_KEYWORDS | Methylation | 3 | 0.520 | 1.71 | 1.00 | 0.99 | 99.98 | |
| UP_KEYWORDS | Ubl conjugation | 4 | 0.551 | 1.37 | 1.00 | 0.99 | 99.99 | ||
| UP_KEYWORDS | DNA-binding | 3 | 0.832 | 0.93 | 1.00 | 1.00 | 100.00 | ||
| Annotation Cluster 6 | INTERPRO | IPR000276:G protein-coupled receptor, rhodopsin-like | 3 | 0.978 | 0.54 | 1.00 | 1.00 | 100.00 | |
| (0.002) | UP_KEYWORDS | G-protein coupled receptor | 3 | 0.985 | 0.50 | 1.00 | 1.00 | 100.00 | |
| INTERPRO | IPR017452:GPCR, rhodopsin-like, 7TM | 3 | 0.985 | 0.50 | 1.00 | 1.00 | 100.00 | ||
| UP_KEYWORDS | Transducer | 3 | 0.988 | 0.48 | 1.00 | 1.00 | 100.00 | ||
The enrichment analysis on differentially exposed genes (DEG) was performed with DAVID Functional annotation software using a high stringency. Depicted here for the upregulated DEGs are two distinctive annotation clusters (enrichment score shown in parenthesis) and six clusters for the downregulated list, with their respective functional terms, number of genes associated with each term (count), statistical significance (*p < 0.05), fold enrichment (FE) and false discovery rate (FDR).