Table 1.
KEGG pathways significant for both statistical tests used in functional class scoring analysis implemented in the Gene Set Comparison Tool of BRB-Array Tools.1
| KEGG Pathway Description | KEGG Pathway |
Number of genes |
LS p value |
LS FDR p-value |
KS pvalue |
KS FDR p-value |
|---|---|---|---|---|---|---|
| Purine metabolism | hsa00230 | 195 | 1.00E-05 | 1.67E-04 | 1.01E-03 | 7.33E-03 |
| Pyrimidine metabolism | hsa00240 | 121 | 1.00E-05 | 1.67E-04 | 3.75E-03 | 2.40E-02 |
| One carbon pool by folate | hsa00670 | 18 | 1.00E-05 | 1.67E-04 | 7.70E-04 | 6.43E-03 |
| Reductive carboxylate cycle (CO2 fixation) | hsa00720 | 16 | 1.00E-05 | 1.67E-04 | 1.00E-05 | 1.67E-04 |
| Atrazine degradation | hsa00791 | 12 | 1.00E-05 | 1.67E-04 | 5.21E-03 | 3.11E-02 |
| Ribosome | hsa03010 | 143 | 1.00E-05 | 1.67E-04 | 1.00E-05 | 1.67E-04 |
| Proteasome | hsa03050 | 41 | 1.00E-05 | 1.67E-04 | 1.00E-05 | 1.67E-04 |
| Cytokine-cytokine receptor interaction | hsa04060 | 256 | 1.00E-05 | 1.67E-04 | 1.00E-05 | 1.67E-04 |
| Cell cycle | hsa04110 | 162 | 1.00E-05 | 1.67E-04 | 1.00E-05 | 1.67E-04 |
| Hematopoietic cell lineage | hsa04640 | 106 | 1.00E-05 | 1.67E-04 | 1.00E-05 | 1.67E-04 |
| Folate biosynthesis | hsa00790 | 49 | 2.00E-05 | 2.78E-04 | 2.42E-03 | 1.62E-02 |
| Citrate cycle (TCA cycle) | hsa00020 | 40 | 2.00E-05 | 2.78E-04 | 1.00E-05 | 1.67E-04 |
| Cell adhesion molecules (CAMs) | hsa04514 | 136 | 5.00E-05 | 6.42E-04 | 1.00E-05 | 1.67E-04 |
| Colorectal cancer | hsa05210 | 111 | 1.20E-04 | 1.43E-03 | 3.88E-03 | 2.40E-02 |
| Synthesis and degradation of ketone bodies | hsa00072 | 8 | 2.00E-04 | 2.23E-03 | 8.00E-05 | 1.03E-03 |
| Phenylalanine, tyrosine and tryptophan biosynthesis | hsa00400 | 12 | 2.70E-04 | 2.82E-03 | 1.00E-05 | 1.67E-04 |
| Prion disease | hsa05060 | 14 | 3.10E-04 | 3.05E-03 | 1.70E-04 | 2.03E-03 |
| TGF-beta signaling pathway | hsa04350 | 94 | 4.40E-04 | 4.08E-03 | 2.07E-03 | 1.44E-02 |
| Oxidative phosphorylation | hsa00190 | 130 | 4.70E-04 | 4.09E-03 | 1.00E-05 | 1.67E-04 |
| Tryptophan metabolism | hsa00380 | 107 | 8.70E-04 | 6.68E-03 | 8.00E-05 | 1.03E-03 |
| Butanoate metabolism | hsa00650 | 50 | 9.20E-04 | 6.68E-03 | 2.10E-04 | 2.34E-03 |
| Propanoate metabolism | hsa00640 | 49 | 9.80E-04 | 6.82E-03 | 7.00E-05 | 1.03E-03 |
| Jak-STAT signaling pathway | hsa04630 | 179 | 1.76E-03 | 1.18E-02 | 3.50E-04 | 3.63E-03 |
| Aminoacyl-tRNA biosynthesis | hsa00970 | 34 | 2.49E-03 | 1.60E-02 | 3.70E-04 | 3.63E-03 |
Abbreviations are as follows: KEGG, Kyoto Encyclopedia of Genes and Genomes; LS, refers to Fisher least significance statistic; KS, refers to Kolmogorov-Smirnov statistic; FDR, refers to false discovery rate and was corrected using the Benjamini and method. The Number of genes column refers to the total number of genes assigned to the pathway.