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Table 5 The top ten genes for 8 diseases with a reasonable training set

From: ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

Prostate cancer    Gastric cancer   
CDKN2A(1029) 210 1 EGFR(1956) 853 1
AKT1(207) 1058 1 AKT1(207) 272 0
IGF1R(3480) 152 1 EXT1(2131) 4 0
MSX1(4487) 5 0 FAS(355) 180 0
PAX3(5077) 2 0 LRP5(4041) 8 0
CCND1(595) 372 1 MSX1(4487) 3 0
BRAF(673) 22 1 CCND1(595) 250 1
TP53(7157) 1378 1 BRAF(673) 32 1
WFS1(7466) 0 0 TP53(7157) 1593 1
WT1(7490) 37 1 WFS1(7466) 0 0
Colorectal cancer    Leukemia acute myeloid   
CDKN2A(1029) 415 1 AKT1(207) 233 0
EXT1(2131) 14 0 FAS(355) 136 0
IGF1R(3480) 86 1 KRAS(3845) 457 1
SMAD4(4089) 211 1 LYN(4067) 26 0
MLH1(4292) 4064 1 MYC(4609) 381 0
PDGFRA(5156) 19 1 RAF1(5894) 30 1
PDGFRB(5159) 45 1 STAT3(6774) 95 0
BRAF(673) 430 1 STK11(6794) 2 0
WFS1(7466) 0 1 BTK(695) 6 0
WT1(7490) 15 0 TP53(7157) 474 1
Diabetes mellitus    Breast cancer   
COL1A1(1277) 4 0 CDKN2A(1029) 572 1
COL2A1(1280) 6 0 COL2A1(1280) 9 0
CYP3A5(1577) 5 0 COL3A1(1281) 1 0
EXT1(2131) 20 1 EXT1(2131) 22 0
GHR(2690) 49 0 LRP5(4041) 51 0
ABCC6(368) 43 0 MSX1(4487) 10 0
LEP(3952) 754 1 PAX3(5077) 6 0
LRP5(4041) 58 0 PITX2(5308) 310 1
CACNA1S(779) 4 0 BRAF(673) 37 1
ADIPOQ(9370) 1635 1 WFS1(7466) 4 0
Alzheimer    Schizophrenia   
COL2A1(1280) 0 0 COL1A1(1277) 0 0
CYP1B1(1545) 0 0 COL2A1(1280) 0 0
EXT1(2131) 4 1 ATN1(1822) 40 0
ALDH3A2(224) 4 0 EXT1(2131) 20 0
APOE(348) 4143 1 FGFR3(2261) 78 0
ABCC6(368) 10 0 GJB1(2705) 0 0
LRP5(4041) 3 0 ABCC6(368) 7 0
MAOA(4128) 5 1 LRP5(4041) 4 0
PSEN2(5664) 635 1 PARK2(5071) 1 0
WFS1(7466) 1 0 WFS1(7466) 5 0
  1. These diseases are in order: prostate cancer [MIM 176807], colorectal cancer [MIM 114500], diabetes mellitus [MIM 125853], Alzheimer [MIM 104300], gastric cancer [MIM 137215], leukemia acute myeloid [MIM 601626], breast cancer [MIM 114480], schizophrenia [MIM 181500]. Using GeneValorization, we counted the number of publication hits in NCBI which are found to be relevant to a query disease and a query gene. At last, the third column indicates whether the gene belongs to the list extracted from the Ingenuity Pathways Analysis tool.