gene plus 99 nearest neighboring genes based on their location on the same chromosome. ToppGene and ToppNet prioritization results are presented in Table 2. ToppGene ranked 19 of 20 (95%) candidate genes within the top 20%, while ToppNet ranked 12 of 16 (75%) candidate genes among the top 20%. The mean ranks for ToppGene- and ToppNet-based prioritization were 6.8 and 11.75, respectively (excluding four disease genes that lacked interaction data). Table 2.Results of the 20 genetic disease prioritizations using ToppGene and ToppNetDiseaseReferenceGeneToppGene rankToppNet rankBipolar disorderLe-Niculescu et al. (35)KLF12215Bipolar disorderLe-Niculescu et al. (35)RORB418Bipolar disorderLe-Niculescu et al. (35)RORA713Bipolar disorderLe-Niculescu et al. (35)ALDH1A110No interaction dataBipolar disorderLe-Niculescu et al. (35)AK3L111No interaction dataCardiomyopathyDhandapany et al. (36)MYBPC312Celiac diseaseHunt et al. (37)SH2B318Celiac diseaseHunt et al. (37)CCR323Celiac diseaseHunt et al. (37)IL18R1329Celiac diseaseHunt et al. (37)RGS1926Celiac diseaseHunt et al. (37)TAGAP14No interaction dataCeliac diseaseHunt et al. (37)IL12A1410Crohns diseaseFisher et al. (38)MST1127Crohns diseaseFisher et al. (38)NKX2-3127Crohns diseaseFisher et al. (38)IRGM2No interaction dataCrohns diseaseVillani et al. (39)NLRP351Crohns diseaseFisher et al. (38)IL12B71Crohns diseaseBarrett et al. (40) Franke et al. (41)STAT3111Crohns diseaseFranke et al. (41)PTPN2306ObesityRenstrom et al. (42)MC4R11Mean6.811.75The gene-disease associations were from recently reported GWAS and include novel disease gene associations. The training sets were compiled using ‘phenotype/disease’ annotations in NCBI's Entrez Gene records
