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Table 1 Enrichment of genes encoding protein kinases, transcription factors, and genes linked to these categories in the global network

From: Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis

  Driver mutations GO term No. of genes No. of network edges, total No. of shared genes FDR(GSEA) No. of network links FDR(NEA)
Set Type No. of genes No. of network edges, total Title
GBM Point mutations 277 40863 Protein kinase activity 277 49534 50 1.10e-63 3680 0.00e + 00
Point mutations 277 40863 Regulation of transcription, DNA dependent 453 84621 19 1.05e-05 2340 1.14e-40
Copy number 455 49817 Protein kinase activity 277 49534 32 2.79e-18 3379 0.00e + 00
Copy number 455 49817 Regulation of transcription, DNA dependent 453 84621 40 2.99e-16 2817 1.87e-44
OV Point mutations 1611 168022 Protein kinase activity 277 49534 103 1.52e-50 10941 0.00e + 00
Point mutations 1611 168022 Regulation of transcription, DNA-dependent 453 84621 93 8.99e-19 9766 0.00e + 00
Copy number 168 24513 Protein kinase activity 277 49534 12 1.71e-07 1247 0.00e + 00
Copy number 168 24513 Regulation of transcription, DNA-dependent 453 84621 7 0.29 1289 1.15e-11
  1. FDR (GSEA): significance for fractions of PK and TF as shared genes.
  2. FDR (NEA): significance for fractions of genes connected to PK and TF in the network.