Table 2. KEGG gene sets enriched in colorectal lesions.
| KEGG Enriched Pathway | P-value | Benjamini-Hochberg | FoldEnrichment | Number ofGenes in thePathway | Number ofDeregulatedGenes | Percentage ofDeregulatedGenes |
| Colorectal Adenoma vs . Normal | ||||||
| Complement and coagulation cascades | 5.6E-08 | 1.0E-05 | 3.29 | 69 | 26 | 38% |
| Cytokine-cytokine receptor interaction | 3.4E-05 | 3.1E-03 | 1.76 | 262 | 53 | 20% |
| Chemokine signaling pathway | 5.0E-04 | 3.0E-02 | 1.77 | 187 | 38 | 20% |
| Viral myocarditis | 2.1E-03 | 9.3E-02 | 2.21 | 71 | 18 | 25% |
| Drug metabolism | 2.4E-03 | 8.4E-02 | 2.64 | 43 | 13 | 30% |
| Intestinal immune network for IgA production | 2.7E-03 | 7.7E-02 | 2.49 | 49 | 14 | 29% |
| Hematopoietic cell lineage | 3.3E-03 | 8.1E-02 | 2.03 | 86 | 20 | 23% |
| Focal adhesion | 3.7E-03 | 8.1E-02 | 1.61 | 201 | 37 | 18% |
| Aldosterone-regulated sodium reabsorption | 5.1E-03 | 9.7E-02 | 2.55 | 41 | 12 | 29% |
| Axon guidance | 5.3E-03 | 9.1E-02 | 1.76 | 129 | 26 | 20% |
| Androgen and oestrogen metabolism | 7.0E-03 | 1.1E-01 | 2.59 | 37 | 11 | 30% |
| Cell adhesion molecules (CAMs) | 7.1E-03 | 1.0E-01 | 1.72 | 132 | 26 | 20% |
| Pentose and glucuronate interconversions | 1.2E-02 | 1.6E-01 | 3.39 | 18 | 7 | 39% |
| ECM-receptor interaction | 1.3E-02 | 1.5E-01 | 1.87 | 84 | 18 | 21% |
| Asthma | 1.4E-02 | 1.5E-01 | 2.71 | 29 | 9 | 31% |
| Pathways in cancer | 1.9E-02 | 1.9E-01 | 1.36 | 328 | 51 | 16% |
| Basal cell carcinoma | 1.9E-02 | 1.9E-01 | 2.06 | 55 | 13 | 24% |
| Leukocyte transendothelial migration | 2.5E-02 | 2.3E-01 | 1.63 | 118 | 22 | 19% |
| Colorectal cancer | 2.7E-02 | 2.3E-01 | 1.77 | 84 | 17 | 20% |
| Folate biosynthesis | 2.9E-02 | 2.3E-01 | 3.96 | 11 | 5 | 45% |
| Ascorbate and aldarate metabolism | 3.7E-02 | 2.8E-01 | 3.08 | 17 | 6 | 35% |
| Sulfur metabolism | 4.0E-02 | 2.8E-01 | 3.63 | 12 | 5 | 42% |
| Prion diseases | 4.0E-02 | 2.8E-01 | 2.24 | 35 | 9 | 26% |
| Nitrogen metabolism | 4.0E-02 | 2.7E-01 | 2.65 | 23 | 7 | 30% |
| p53 signaling pathway | 4.2E-02 | 2.7E-01 | 1.80 | 68 | 14 | 21% |
| Colorectal Cancer vs . Normal | ||||||
| Cell cycle | 2.2E-07 | 3.9E-05 | 2.96 | 125 | 29 | 23% |
| DNA replication | 9.9E-06 | 8.9E-04 | 4.60 | 36 | 13 | 36% |
| Pentose and glucuronate interconversions | 2.5E-04 | 1.5E-02 | 5.66 | 18 | 8 | 44% |
| Purine metabolism | 7.0E-04 | 3.1E-02 | 2.08 | 153 | 25 | 16% |
| Oocyte meiosis | 2.0E-03 | 6.9E-02 | 2.20 | 110 | 19 | 17% |
| p53 signaling pathway | 2.0E-03 | 5.8E-02 | 2.62 | 68 | 14 | 21% |
| Drug metabolism | 2.7E-03 | 6.6E-02 | 2.67 | 62 | 13 | 21% |
| Starch and sucrose metabolism | 4.4E-03 | 9.4E-02 | 3.03 | 42 | 10 | 24% |
| Mismatch repair | 7.1E-03 | 1.3E-01 | 3.88 | 23 | 7 | 30% |
| Nitrogen metabolism | 7.1E-03 | 1.3E-01 | 3.88 | 23 | 7 | 30% |
| Ascorbate and aldarate metabolism | 8.1E-03 | 1.4E-01 | 4.50 | 17 | 6 | 35% |
| Sulfur metabolism | 1.1E-02 | 1.7E-01 | 5.31 | 12 | 5 | 42% |
| Pyramiding metabolism | 1.5E-02 | 2.0E-01 | 2.01 | 95 | 15 | 16% |
| Progesterone-mediated acolyte maturation | 1.5E-02 | 1.9E-01 | 2.07 | 86 | 14 | 16% |
| Drug metabolism | 1.7E-02 | 1.9E-01 | 2.67 | 43 | 9 | 21% |
| Metabolism of xenobiotics by cytochrome P | 1.7E-02 | 1.8E-01 | 2.34 | 60 | 11 | 18% |
| Androgen and estrogen metabolism | 2.3E-02 | 2.3E-01 | 2.76 | 37 | 8 | 22% |
| Retinol metabolism | 2.3E-02 | 2.2E-01 | 2.36 | 54 | 10 | 19% |
| Steroid hormone biosynthesis | 2.5E-02 | 2.2E-01 | 2.49 | 46 | 9 | 20% |
| Glycine, serine and threonine metabolism | 3.0E-02 | 2.5E-01 | 2.88 | 31 | 7 | 23% |
| Colorectal Cancer vs . Colorectal Adenoma | ||||||
| ECM-receptor interaction | 5.6E-05 | 7.8E-03 | 4.12 | 84 | 13 | 15% |
| TGF-beta signaling pathway | 7.9E-05 | 5.6E-03 | 3.98 | 87 | 13 | 15% |
| Focal adhesion | 1.5E-04 | 7.2E-03 | 2.65 | 201 | 20 | 10% |
| Complement and coagulation cascades | 3.9E-03 | 1.3E-01 | 3.47 | 69 | 9 | 13% |
| Arginine and proline metabolism | 4.7E-02 | 7.4E-01 | 3.01 | 53 | 6 | 11% |
The KEGG pathway analysis showed 25 gene sets distinguishing CRA from NOR, 20 distinguishing CRC from NOR, and five distinguishing CRC from CRA (P-value ≤0.05), considering deregulated genes with a 2-fold cut-off difference (P-value ≤0.01 by t-test with FDR).