Table 9

Enrichment analysis of the top scored subnetworks
Stage Biological Process p-value Genes in subnetworks
Common across all Stages Activation of MAPKK activity 1.12E-03 PHOX2A*, HAND2*, PPP2R5D, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAP1A
I & II Co-SMAD binding 1.2E-05 FOXG1*, FOXH1, SMAD2, SMAD1, MED15, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAP1A
II & III Nerve growth factor receptor signaling pathways 2.21E-04 HOXD4*, INPP5B, SLC6A2, STX1A, VAMP1, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAPIA
I & III Positive regulation of peptidyl-serine phosphorylation 1.42E-03 NPY*, NPY1R, LSM7, NR1H2, RMI1, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF
I Transmembrane receptor protein tyrosine kinase signaling pathway 1.87E-03 HLA-G*, COPB1, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAP1A
II DNA helicase complex 6.8E-05 SERPINB5*, UCHL5, ACTR8, ACTR5, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF
III Nerve growth factor receptor signaling pathway 5.5E-04 HOXB4*, CREBBP, KLF13, UBC, KRAS, PIK3CA, PIK3R3, RAF1, BRAF, RAP1A

*: commonality with Table 2.

Pradhan et al.

Pradhan et al. BMC Systems Biology 2013 7:141   doi:10.1186/1752-0509-7-141

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