Table 3. Enrichment analysis of the brown module genes.
| Term | P | adj.P | Odd Ratio | Combined Score a |
|---|---|---|---|---|
| Type I interferon signaling pathway (GO:0060337) | 6.14 x 10−9 | 1.05 x 10−5 | 10.6 | 200.0 |
| Regulation of interleukin-8 secretion (GO:2000482) | 2.70 x 10−5 | 0.01 | 13.6 | 142.9 |
| Positive regulation of response to cytokine stimulus (GO:0060760) | 5.67 x 10−5 | 0.02 | 17.9 | 174.6 |
| Response to interferon-alpha (GO:0035455) | 1.30 x 10−4 | 0.03 | 14.7 | 131.6 |
| Positive regulation of interleukin-6 secretion (GO:2000778) | 1.30 x 10−4 | 0.03 | 14.7 | 131.6 |
| Positive regulation of interferon-alpha production (GO:0032727) | 2.06 x 10−4 | 0.04 | 13.2 | 111.7 |
| Regulation of dendritic cell apoptotic process (GO:2000668) | 4.48 x 10−4 | 0.05 | 18.8 | 144.6 |
| Positive regulation of tumor necrosis factor secretion (GO:1904469) | 6.09 x 10−4 | 0.07 | 17.0 | 126.2 |
| Ribose phosphate metabolic process (GO:0019693) | 8.02 x 10−4 | 0.08 | 15.6 | 111.4 |
| Pentose-phosphate shunt (GO:0006098) | 8.02 x 10−4 | 0.08 | 15.6 | 111.4 |
| Response to chemokine (GO:1990868) | 0.004 | 0.19 | 20.8 | 116.8 |
| Cellular response to chemokine (GO:1990869) | 0.004 | 0.19 | 20.8 | 116.8 |
| Positive regulation of ATP biosynthetic process (GO:2001171) | 0.004 | 0.18 | 20.8 | 116.8 |
| Vesicle fusion with endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane (GO:1990668) | 0.004 | 0.18 | 20.8 | 116.8 |
| Antigen processing and presentation of endogenous peptide antigen (GO:0002483) | 0.004 | 0.18 | 20.8 | 116.8 |
| Regulation of blood vessel remodelling (GO:0060312) | 0.004 | 0.18 | 20.8 | 116.8 |
| Regulation of interleukin-12 secretion (GO:2001182) | 0.004 | 0.18 | 20.8 | 116.8 |
| Regulation of interferon-alpha secretion (GO:1902739) | 0.004 | 0.17 | 20.8 | 116.8 |
| Positive regulation of interferon-alpha secretion (GO:1902741) | 0.004 | 0.17 | 20.8 | 116.8 |
| Glomerulus vasculature development (GO:0072012) | 0.004 | 0.17 | 20.8 | 116.8 |
Results shows the top 20 gene ontology (GO) of biological processes based on combined score.
a
The expected mean rank and standard deviation was calculated from running the Fisher exact test for many random gene sets for each term in the gene-set library and then the z-score was calculated to assess the deviation from the expected rank for the enriched GO term for the genes in the module. Finally, the combined score was computed by multiplying the z-score by the negative log of the p-value from the Fisher exact test.