Skip to main content

Advertisement

Table 2 Average number of gene predictions made by Gentrepid modes and modules

From: Analysis of genome-wide association study data using the protein knowledge base

Mode SNP/gene CPS CMP CPS + CMP
  Approach WS MWS MHS HS WS MWS MHS HS WS MWS MHS HS
Seeded BY 1 Mbp 29.14 6.00 2.29 0.71 15.43 3.86 0.71 0.43 42.86 9.43 3.00 1.14
   0.5 Mbp 12.29 5.29 2.00 1.29 9.00 2.86 0.57 0.29 20.71 7.71 2.57 1.57
   0.1 Mbp 6.71 3.00 1.71 1.00 3.14 1.00 0.29 0.00 9.57 3.57 1.86 1.00
  NN Adjacent 19.14 6.00 1.57 1.43 6.86 1.57 0.43 0.00 25.29 7.00 1.86 1.43
   Nearest 10.86 2.57 1.43 1.00 3.00 0.86 0.29 0.00 13.71 3.29 1.57 1.00
   Resident 4.29 1.43 1.00 0.57 1.29 0.43 0.14 0.00 5.57 1.86 1.14 0.57
Ab initio BY 1 Mbp 105.00 27.14 6.86 5.86 57.57 14.71 12.57 10.14 157.14 40.71 17.43 14.29
   0.5 Mbp 41.29 17.43 5.86 2.86 30.71 12.71 8.57 10.43 70.00 29.57 14.43 11.86
   0.1 Mbp 28.57 6.71 2.00 0.57 12.14 10.00 7.86 3.57 38.14 16.71 9.86 4.14
  NN Adjacent 59.57 13.86 2.14 0.71 26.86 8.71 5.29 2.00 81.14 21.29 6.71 2.71
   Nearest 28.71 5.14 1.00 0.57 10.86 2.00 1.71 0.00 37.43 6.86 2.71 0.57
   Resident 13.00 2.57 0.29 0.00 9.71 0.86 0.57 0.00 21.00 3.14 0.86 0.00
Seeded and ab initio BY 1 Mbp 105.00 27.14 6.86 6.57 72.43 18.43 13.29 10.57 170.14 44.00 18.14 15.43
   0.5 Mbp 41.43 17.43 5.86 3.57 39.57 15.57 9.14 10.71 78.43 32.00 15.00 12.86
   0.1 Mbp 28.57 7.00 2.29 1.29 15.29 11.00 8.14 3.57 40.57 17.57 10.29 4.86
  NN Adjacent 59.57 13.86 2.29 1.71 33.43 10.29 5.71 2.00 86.57 22.29 7.14 3.71
   Nearest 28.71 5.29 1.71 1.14 13.86 2.86 2.00 0.00 39.86 7.57 3.57 1.14
   Resident 13.00 2.71 1.00 0.57 10.71 1.29 0.71 0.00 22.00 3.71 1.71 0.57
  1. Each cell represents the number of predictions averaged across the seven phenotypes made by the mode and module. Column abbreviations: HS, highly significant; MHS, moderately-high significance; MWS, moderately-weak significance; WS, weakly significant; CPS, common pathway scanning module; CMP, common module profiling. Row abbreviations: Seeded, mode using known disease gene information as seeds; Ab initio, blind approach mode; BY, bystander approach; NN, nearest neighbour approach. The total number of predictions made by Gentrepid for each significance threshold and SNP/gene approach are bolded. All results have been filtered on significance. For CPS, pathways reach a significance threshold of p < 0.05 based on Fishers exact test. For CMP seeded, a threshold of 0.4. For CMP ab initio, a threshold of χ2 max_unique > 105 and χ2 min > 7.88 for multidomain proteins and χ2 min > 100 for single domain proteins.