TABLE 1

All pathways with nominal P ≤ 0.05 in WTCCC data

DatabasePathwaySizeP(Padj)False discovery rate
KEGGWNT signaling pathway1260.0007 (0.31)0.20
KEGGOlfactory transduction260.0009 (0.4)0.37
GOOrganic acid biosynthetic process300.004 (1)0.60
GORegulation of Wnt receptor signaling pathway240.005 (1)0.51
GOOdontogenesis220.005 (1)0.54
GOAminoglycan metabolic process320.007 (1)0.53
GOMembrane invagination620.009 (1)0.51
GOCalcium-dependent cell-cell adhesion200.01 (1)0.60
KEGGGalactose metabolism260.01 (1)0.53
BioCartaALK in cardiac myocytes320.01 (1)0.46
GOBiomineral formation300.02 (1)0.64
GOEndocytosis1310.02 (1)0.64
GOGonad development220.02 (1)0.63
GOSensory organ development590.03 (1)0.74
BioCartaWNT signaling pathway200.03 (1)0.72
KEGGPyruvate metabolism380.03 (1)0.76
GOMonosaccharide metabolic process1150.03 (1)0.78
GOCysteine-type peptidase activity1140.03 (1)0.77
GOCarbohydrate biosynthetic process730.04 (1)0.82
GOGABA receptor activity200.04 (1)0.81
KEGGType II diabetes360.04 (1)0.82
GOPositive regulation of transport260.04 (1)0.78
KEGGTGF-β signaling pathway730.04 (1)0.79
GOEpidermal cell differentiation450.05 (1)0.75
GOEpidermis morphogenesis450.05 (1)0.75
BioCartaRegulation of PGC-1a HDAC5210.05 (1)0.82
  • Results based on 10,000 permutations and 439 pathways. Gene size is the number of analyzed genes within that pathway. Padjis the Bonferroni-adjusted P value based on 439 statistical tests. GO, Gene Ontology.