Table 8.
Top 10 KEGG pathways by count as determined by Transcriptome Analysis Console (TAC) software 1.
| Pathway | #Total | #Up | #Down | Significance | p-Value | |
|---|---|---|---|---|---|---|
| HIV-Drug- | PI3K-Akt Signaling Pathway | 20 | 13 | 7 | 0 | 1 |
| Focal Adhesion-PI3K-Akt-mTOR-signaling pathway | 20 | 13 | 7 | 0.21 | 0.62234 | |
| VEGFA-VEGFR2 Signaling Pathway | 20 | 12 | 8 | 0.9 | 0.127165 | |
| Nuclear Receptors Meta-Pathway | 20 | 11 | 9 | 0.09 | 0.811647 | |
| Regulation of toll-like receptor signaling pathway | 19 | 10 | 9 | 2.84 | 0.001437 | |
| MAPK Signaling Pathway | 18 | 9 | 9 | 0.47 | 0.3394 | |
| miR-targeted genes in muscle cell—TarBase | 17 | 7 | 10 | 0.93 | 0.116256 | |
| miR-targeted genes in lymphocytes—TarBase | 17 | 7 | 10 | 2 | 0.009973 | |
| Toll-like Receptor Signaling Pathway | 15 | 9 | 6 | 2.96 | 0.001086 | |
| Olfactory receptor activity | 15 | 12 | 3 | 1 | 0.100786 | |
| HIV-Drug+ | PI3K-Akt Signaling Pathway | 35 | 8 | 27 | 0.11 | 0.783262 |
| miR-targeted genes in lymphocytes—TarBase | 34 | 3 | 31 | 1.89 | 0.012864 | |
| miR-targeted genes in muscle cell—TarBase | 32 | 3 | 29 | 0.87 | 0.136266 | |
| Focal Adhesion-PI3K-Akt-mTOR-signaling pathway | 30 | 8 | 22 | 0.03 | 0.922794 | |
| Olfactory receptor activity | 24 | 8 | 16 | 1.82 | 0.015221 | |
| Nuclear Receptors Meta-Pathway | 24 | 6 | 18 | 0.8 | 0.157659 | |
| VEGFA-VEGFR2 Signaling Pathway | 22 | 7 | 15 | 0.08 | 0.827347 | |
| miR-targeted genes in epithelium—TarBase | 22 | 3 | 19 | 1.72 | 0.01896 | |
| Genes related to primary cilium development (based on CRISPR) | 21 | 1 | 20 | 2.73 | 0.001861 | |
| Ciliary landscape | 21 | 0 | 21 | 0 | 1 | |
| HIV+Drug- | miR-targeted genes in lymphocytes—TarBase | 46 | 8 | 38 | 0.87 | 0.134124 |
| Nuclear Receptors Meta-Pathway | 41 | 17 | 24 | 0.43 | 0.372732 | |
| PI3K-Akt Signaling Pathway | 40 | 14 | 26 | 0.14 | 0.728467 | |
| miR-targeted genes in muscle cell—TarBase | 38 | 8 | 30 | 0.74 | 0.183176 | |
| MAPK Signaling Pathway | 37 | 11 | 26 | 1.18 | 0.065447 | |
| Focal Adhesion-PI3K-Akt-mTOR-signaling pathway | 35 | 15 | 20 | 0.11 | 0.783054 | |
| VEGFA-VEGFR2 Signaling Pathway | 35 | 12 | 23 | 1.01 | 0.097823 | |
| miR-targeted genes in epithelium—TarBase | 29 | 7 | 22 | 1.06 | 0.087395 | |
| Breast cancer pathway | 26 | 8 | 18 | 1.54 | 0.029057 | |
| Circadian rhythm related genes | 26 | 7 | 19 | 0.3 | 0.50212 | |
| HIV+Drug+ | Nuclear Receptors Meta-Pathway | 43 | 29 | 14 | 0.67 | 0.211976 |
| PI3K-Akt Signaling Pathway | 42 | 17 | 25 | 0.31 | 0.487261 | |
| miR-targeted genes in lymphocytes—TarBase | 42 | 9 | 33 | 1.42 | 0.038159 | |
| Focal Adhesion-PI3K-Akt-mTOR-signaling pathway | 37 | 16 | 21 | 0.28 | 0.520416 | |
| VEGFA-VEGFR2 Signaling Pathway | 36 | 18 | 18 | 1.2 | 0.062498 | |
| miR-targeted genes in muscle cell—TarBase | 34 | 10 | 24 | 1.38 | 0.041842 | |
| miR-targeted genes in epithelium—TarBase | 27 | 8 | 19 | 1.48 | 0.032898 | |
| MAPK Signaling Pathway | 26 | 11 | 15 | 0.08 | 0.838897 | |
| TGF-beta Signaling Pathway | 25 | 10 | 15 | 1.9 | 0.012623 | |
| Ciliary landscape | 23 | 8 | 15 | 0.04 | 0.913439 |
1 Gene expression parameters were as follows: Gene-level fold change < −2 or > 2; gene-level p-value < 0.05, gene-level FDR < 0.05, ANOVA statistical analysis with eBayes correction. The Pos/Neg Area Under the Curve (AUC) threshold was set to 0.7. Gene-level Signal Space Transformation-Robust Multi-Chip Analysis (SST-RMA) method was used for summarization.