Table 2.
Downregulated signaling pathways upon HGF stimulation in Detroit 562. Ranking based on adjusted p-value (p.adjust). Results of the first seven pathways on the list and of two pathways of interest are shown. Only genes that are part of at least one of the pathways listed in KEGG and that show a difference in expression of ≤ −0.4 (log2 fold change) and padj < 0.1 are included.
| Rank | ID 1 | Description | GeneRatio 2 | BgRatio 3 | p.adjust 4 |
|---|---|---|---|---|---|
| 1 | hsa05204 | Chemical carcinogenesis | 28/763 | 82/7946 | 2.7 × 10−7 |
| 2 | hsa00980 | Metabolism of xenobiotics by cytochrome P450 | 24/763 | 76/7946 | 1.2 × 10−5 |
| 3 | hsa00053 | Ascorbate and aldarate metabolism | 12/763 | 27/7946 | 0.0002 |
| 4 | hsa00860 | Porphyrin and chlorophyll metabolism | 15/763 | 42/7946 | 0.0003 |
| 5 | hsa00140 | Steroid hormone biosynthesis | 18/763 | 60/7946 | 0.0005 |
| 6 | hsa05322 | Systemic lupus erythematosus | 29/763 | 133/7946 | 0.0009 |
| 7 | hsa00982 | Drug metabolism—cytochrome P450 | 19/763 | 72/7946 | 0.0014 |
| 86 | hsa00010 | Glycolysis/Gluconeogenesis | 10/763 | 68/7946 | 0.4096 |
| 113 | hsa05230 | Central carbon metabolism in cancer | 9/763 | 69/7946 | 0.5790 |
| Total 311 |
1 ID: identification number of the pathway at Kyoto Encyclopedia of Genes and Genomes (KEGG). 2 GeneRatio: number of upregulated genes in this pathway/total number of upregulated genes. 3 BgRatio: total number of genes in this pathway/total number of genes in KEGG. 4 p.adjust: adjusted p value for indicated pathway.