Table 1 Significant pathways selected from SSC and ASC exome data.

Columns P and q are the P- and q-values from marginal tests, and Pcon and qcon are from the conditional tests. Columns j and k are the marginal and conditional counts of selected genes. These pathways are likely drivers or disease-causing pathways because of the special analysis procedure (Materials and Methods). See table S4 for full lists of selected variants and genes.

PqPconqconjkReference
SSC pathways
  hsa00310 Lysine degradation8.0 × 10−50.028.0 × 10−50.0288(11, 44)
  hsa04727 GABAergic synapse4.9 × 10−30.313.9 × 10−30.0388(45, 46)
  hsa04974 Protein digestion and absorption1.5 × 10−20.359.7 × 10−30.0777(35)
  hsa04310 Wnt signaling pathway7.9 × 10−30.318.5 × 10−30.08109(47, 48)
  hsa04810 Regulation of actin cytoskeleton2.5 × 10−20.356.3 × 10−30.061212(49, 50)
  hsa04010 MAPK signaling pathway2.1 × 10−20.359.1 × 10−30.071410(51, 52)
  hsa04530 Tight junction1.7 × 10−20.356.6 × 10−20.1795(53, 54)
  hsa04713 Circadian entrainment7.7 × 10−30.316.6 × 10−20.1483(34, 55)
  hsa04724 Glutamatergic synapse2.1 × 10−20.351.9 × 10−10.1982(56, 57)
ASC pathways
  hsa00310 Lysine degradation6.2 × 10−50.016.2 × 10−50.0155(11, 44)
  hsa04713 Circadian entrainment1.5 × 10−30.159.9 × 10−40.0155(34, 55)
  hsa04976 Bile secretion3.5 × 10−30.188.4 × 10−30.0643(35)
  hsa04727 GABAergic synapse7.8 × 10−30.214.4 × 10−20.1242(45, 46)
  hsa04010 MAPK signaling pathway7.1 × 10−30.216.7 × 10−20.0774(51, 52)