Table 3.

Top 10 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways identified by gene set enrichment analysis (GSEA)

Gene set nameNo. of genes in gene set (K)DescriptionNo. of genes in overlap (k)% of MAPK genesFDR q value
KEGG PATHWAYS IN CANCER328Pathways in cancer2528 (7/25)4.63E−9
KEGG NON SMALL CELL LUNG CANCER54Non–small cell lung cancer944 (4/9)7.68E−6
KEGG SMALL CELL LUNG CANCER84Small cell lung cancer1020 (2/10)2.6E−5
KEGG ENDOCYTOSIS183Endocytosis1414 (2/4)2.66E−5
KEGG UBIQUITIN MEDIATED PROTEOLYSIS138Ubiquitin mediated proteolysis128 (1/12)3.51E−5
KEGG MAPK SIGNALING PATHWAY267MAPK signaling pathway16100 (16/16)7.34E−5
KEGG GLIOMA65Glioma838 (3/8)1.25E−4
KEGG MELANOMA71Melanoma838 (3/8)2.14E−4
KEGG ADHERENS JUNCTION75Adherens junction802.86E−4
KEGG SNARE INTERACTIONS IN VESICULAR TRANSPORT38SNARE interactions in vesicular transport603.21E−4
  • NOTE: K, number of genes in the pathway; k, number of genes overlapping with the KEGG pathway. The fraction of genes overlapping with MAPK pathway was based on the genes identified and is presented in Supplementary Table S2. Statistical significance is given as false discovery rate (FDR) q value with q < 0.05 used as cutoff for selection of significant pathways.