Table 1. KEGG pathways overrepresented among genes differentiating control and MCPIP1 and D141N cells.
| ID | Description | GeneRatio | BgRatio | p value | q value | Count | |
|---|---|---|---|---|---|---|---|
| MCPIP1 vs Control | Upregulated | ||||||
| hsa03030 | DNA replication | 18/481 | 32/4312 | 5.61E-10 | 1.45E-07 | 18 | |
| hsa05322 | Systemic lupus erythematosus | 28/481 | 74/4312 | 1.44E-09 | 1.86E-07 | 28 | |
| hsa04110 | Cell cycle | 34/481 | 113/4312 | 2.45E-08 | 2.10E-06 | 34 | |
| hsa05034 | Alcoholism | 34/481 | 125/4312 | 3.74E-07 | 2.41E-05 | 34 | |
| hsa03010 | Ribosome | 32/481 | 118/4312 | 8.97E-07 | 4.63E-05 | 32 | |
| hsa04115 | p53 signaling pathway | 16/481 | 55/4312 | 2.11E-04 | 9.08E-03 | 16 | |
| hsa03430 | Mismatch repair | 8/481 | 20/4312 | 8.42E-04 | 3.10E-02 | 8 | |
| hsa03420 | Nucleotide excision repair | 12/481 | 40/4312 | 9.62E-04 | 3.10E-02 | 12 | |
| Downregulated | |||||||
| hsa04142 | Lysosome | 29/517 | 103/4312 | 5.63E-06 | 1.52E-03 | 29 | |
| hsa04610 | Complement and coagulation cascades | 13/517 | 32/4312 | 3.63E-05 | 4.90E-03 | 13 | |
| D14N vs Control | Upregulated | ||||||
| hsa04110 | Cell cycle | 76/1574 | 116/4752 | 5.18E-13 | 1.45E-10 | 76 | |
| hsa04114 | Oocyte meiosis | 58/1574 | 95/4752 | 1.65E-08 | 2.30E-06 | 58 | |
| hsa04120 | Ubiquitin mediated proteolysis | 63/1574 | 119/4752 | 5.03E-06 | 4.68E-04 | 63 | |
| hsa04914 | Progesterone-mediated oocyte maturation | 41/1574 | 78/4752 | 2.76E-04 | 1.93E-02 | 41 | |
| hsa04141 | Protein processing in endoplasmic reticulum | 70/1574 | 151/4752 | 4.07E-04 | 2.27E-02 | 70 | |
| hsa03430 | Mismatch repair | 15/1574 | 22/4752 | 7.94E-04 | 3.69E-02 | 15 | |
| hsa03420 | Nucleotide excision repair | 24/1574 | 42/4752 | 1.11E-03 | 3.87E-02 | 24 | |
| hsa03013 | RNA transport | 62/1574 | 135/4752 | 1.15E-03 | 3.87E-02 | 62 | |
| hsa03018 | RNA degradation | 35/1574 | 68/4752 | 1.25E-03 | 3.87E-02 | 35 | |
| hsa03460 | Fanconi anemia pathway | 25/1574 | 45/4752 | 1.53E-03 | 4.01E-02 | 25 | |
| hsa03015 | mRNA surveillance pathway | 38/1574 | 76/4752 | 1.58E-03 | 4.01E-02 | 38 | |
| hsa03040 | Spliceosome | 57/1574 | 124/4752 | 1.75E-03 | 4.06E-02 | 57 | |
| Downregulated | |||||||
| hsa04142 | Lysosome | 63/1564 | 113/4752 | 3.61E-07 | 1.03E-04 | 63 | |
| hsa01230 | Biosynthesis of amino acids | 33/1564 | 54/4752 | 1.79E-05 | 2.55E-03 | 33 | |
| hsa04932 | Non-alcoholic fatty liver disease | 64/1564 | 127/4752 | 2.71E-05 | 2.58E-03 | 64 | |
| hsa01200 | Carbon metabolism | 47/1564 | 91/4752 | 1.48E-04 | 1.05E-02 | 47 | |
| hsa00190 | Oxidative phosphorylation | 52/1564 | 104/4752 | 1.96E-04 | 1.12E-02 | 52 | |
| hsa05012 | Parkinson’s disease | 53/1564 | 108/4752 | 3.13E-04 | 1.49E-02 | 53 | |
Terms common for both comparisons are bolded. ID – KEGG identifier, GeneRatio – the ratio of number of differentiating genes in a given pathway to the number of differentiating genes with KEGG identifier ; BgRatio – the ratio of number of not differentiating genes in a given pathway to the number of expressed genes with KEGG identifier; p-value - p-value in hypergeometric test; q-value - p-value after FDR correction; Count – number of differentiating genes contributing to a given pathway.