********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** WARNING: Incorrect mutation M1106I WARNING: Incorrect mutation T1110A WARNING: Incorrect mutation T1110I WARNING: Incorrect mutation V1111I WARNING: Incorrect mutation V1111F WARNING: Incorrect mutation T1113P WARNING: Incorrect mutation T1113I WARNING: Incorrect mutation F1114S WARNING: Incorrect mutation E1115K WARNING: Incorrect mutation E1115G WARNING: Incorrect mutation G1116E WARNING: Incorrect mutation G1116A WARNING: Incorrect mutation Y1122S WARNING: Incorrect mutation R1123S WARNING: Incorrect mutation R1123G WARNING: Incorrect mutation R1123C WARNING: Incorrect mutation R1123H WARNING: Incorrect mutation I1125V WARNING: Incorrect mutation D1126N WARNING: Incorrect mutation T1129M WARNING: Incorrect mutation D1131N WARNING: Incorrect mutation K1132E WARNING: Incorrect mutation G1133S WARNING: Incorrect mutation G1133D WARNING: Incorrect mutation I1135V WARNING: Incorrect mutation I1135M WARNING: Incorrect mutation R1139H WARNING: Incorrect mutation V1140E WARNING: Incorrect mutation I1142L WARNING: Incorrect mutation I1144V WARNING: Incorrect mutation I1147V WARNING: Incorrect mutation I1148T WARNING: Incorrect mutation I1152F WARNING: Incorrect mutation I1153V WARNING: Incorrect mutation A1154T WARNING: Incorrect mutation A1154S WARNING: Incorrect mutation A1154V WARNING: Incorrect mutation M1158K WARNING: Incorrect mutation V1162M WARNING: Incorrect mutation V1162L WARNING: Incorrect mutation I1166T WARNING: Incorrect mutation V1167I WARNING: Incorrect mutation V1167A WARNING: Incorrect mutation T1168N WARNING: Incorrect mutation Q1170R WARNING: Incorrect mutation K1178N WARNING: Incorrect mutation K1184N WARNING: Incorrect mutation V1190M WARNING: Incorrect mutation V1190L WARNING: Incorrect mutation V1190G WARNING: Incorrect mutation A1193T WARNING: Incorrect mutation A1193V WARNING: Incorrect mutation A1196T WARNING: Incorrect mutation R1197W WARNING: Incorrect mutation R1197Q WARNING: Incorrect mutation R1200Q WARNING: Incorrect mutation I1203V WARNING: Incorrect mutation I1203T WARNING: Incorrect mutation K1205E WARNING: Incorrect mutation K1205R WARNING: Incorrect mutation K1205N WARNING: Incorrect mutation Q1209K WARNING: Incorrect mutation Q1209R WARNING: Incorrect mutation Q1209H WARNING: Incorrect mutation Y1210H WARNING: Incorrect mutation K1211E WARNING: Incorrect mutation Y1214H WARNING: Incorrect mutation V1215M WARNING: Incorrect mutation V1215L WARNING: Incorrect mutation V1216I WARNING: Incorrect mutation N1217T WARNING: Incorrect mutation F1221L WARNING: Incorrect mutation F1226S WARNING: Incorrect mutation F1226L WARNING: Incorrect mutation F1226L WARNING: Incorrect mutation V1227I WARNING: Incorrect mutation V1227L WARNING: Incorrect mutation L1231F WARNING: Incorrect mutation I1234V WARNING: Incorrect mutation I1234F WARNING: Incorrect mutation I1234N WARNING: Incorrect mutation I1234T WARNING: Incorrect mutation C1235F WARNING: Incorrect mutation A1237V WARNING: Incorrect mutation M1238V WARNING: Incorrect mutation Y1241S WARNING: Incorrect mutation G1242S WARNING: Incorrect mutation S1244N WARNING: Incorrect mutation F1247L WARNING: Incorrect mutation A1250T WARNING: Incorrect mutation A1250S WARNING: Incorrect mutation M1251T WARNING: Incorrect mutation M1251I WARNING: Incorrect mutation L1254V WARNING: Incorrect mutation N1255S WARNING: Incorrect mutation L1257F WARNING: Incorrect mutation V1264M WARNING: Incorrect mutation V1264L WARNING: Incorrect mutation I1271T WARNING: Incorrect mutation I1271M WARNING: Incorrect mutation F1273L WARNING: Incorrect mutation P1275L WARNING: Incorrect mutation C1280R WARNING: Incorrect mutation C1280F WARNING: Incorrect mutation A1288T WARNING: Incorrect mutation A1288S WARNING: Incorrect mutation L1289W WARNING: Incorrect mutation L1289F WARNING: Incorrect mutation V1292L WARNING: Incorrect mutation I1298M WARNING: Incorrect mutation I1300V WARNING: Incorrect mutation E1302K WARNING: Incorrect mutation H1308Q WARNING: Incorrect mutation T1309N WARNING: Incorrect mutation T1309S WARNING: Incorrect mutation Q1310H WARNING: Incorrect mutation C1311R WARNING: Incorrect mutation S1312P WARNING: Incorrect mutation P1313S WARNING: Incorrect mutation A1317T WARNING: Incorrect mutation I1323V WARNING: Incorrect mutation I1323F WARNING: Incorrect mutation I1323T WARNING: Incorrect mutation T1326P WARNING: Incorrect mutation T1326A WARNING: Incorrect mutation R1329C WARNING: Incorrect mutation R1329H WARNING: Incorrect mutation R1332W WARNING: Incorrect mutation R1332Q WARNING: Incorrect mutation R1335H WARNING: Incorrect mutation V1337G WARNING: Incorrect mutation R1342C WARNING: Incorrect mutation R1342H WARNING: Incorrect mutation G1343A WARNING: Incorrect mutation R1347Q WARNING: Incorrect mutation T1348M WARNING: Incorrect mutation I1354F WARNING: Incorrect mutation L1360V WARNING: Incorrect mutation V1363M WARNING: Incorrect mutation V1363L WARNING: Incorrect mutation V1363L WARNING: Incorrect mutation A1364V WARNING: Incorrect mutation I1367M WARNING: Incorrect mutation V1368M WARNING: Incorrect mutation V1368L WARNING: Incorrect mutation M1369L WARNING: Incorrect mutation A1375T WARNING: Incorrect mutation A1375V WARNING: Incorrect mutation M1379V WARNING: Incorrect mutation A1386S WARNING: Incorrect mutation D1389H WARNING: Incorrect mutation D1389Y WARNING: Incorrect mutation T1390I WARNING: Incorrect mutation T1391A WARNING: Incorrect mutation N1394Y WARNING: Incorrect mutation N1394S WARNING: Incorrect mutation N1396H WARNING: Incorrect mutation T1401S WARNING: Incorrect mutation P1403S WARNING: Incorrect mutation V1406M WARNING: Incorrect mutation V1406L WARNING: Incorrect mutation V1406A WARNING: Incorrect mutation A1413V WARNING: Incorrect mutation G1415E WARNING: Incorrect mutation D1420N WARNING: Incorrect mutation A1424D WARNING: Incorrect mutation C1425Y WARNING: Incorrect mutation P1427A WARNING: Incorrect mutation K1430T WARNING: Incorrect mutation K1430N WARNING: Incorrect mutation K1430N WARNING: Incorrect mutation A1432V WARNING: Incorrect mutation S1435P WARNING: Incorrect mutation E1436K WARNING: Incorrect mutation P1437S WARNING: Incorrect mutation S1438T WARNING: Incorrect mutation S1438I WARNING: Incorrect mutation T1441M WARNING: Incorrect mutation E1442Q WARNING: Incorrect mutation G1443S WARNING: Incorrect mutation T1445I WARNING: Incorrect mutation P1446T WARNING: Incorrect mutation P1446A WARNING: Incorrect mutation P1446S WARNING: Incorrect mutation S1450N WARNING: Incorrect mutation F1451V WARNING: Incorrect mutation A1452S Sequence File: CAC1C_HUMAN.seq Mutation Prediction RI Probability Method I1249F Disease 7 0.869 PhD-SNP: F[I]=81% F[F]=0% Nali=1201 I1249F Disease 10 0.987 PANTHER: F[I]=94% F[F]=0% I1249F Disease 9 0.956 SNPs&GO N1252S Disease 6 0.785 PhD-SNP: F[N]=89% F[S]=4% Nali=1202 N1252S Disease 10 0.989 PANTHER: F[N]=97% F[S]=0% N1252S Disease 8 0.922 SNPs&GO N1252Y Disease 8 0.923 PhD-SNP: F[N]=89% F[Y]=0% Nali=1202 N1252Y Disease 10 0.996 PANTHER: F[N]=97% F[Y]=0% N1252Y Disease 9 0.959 SNPs&GO S1314F Disease 8 0.882 PhD-SNP: F[S]=76% F[F]=0% Nali=602 S1314F Disease 10 0.987 PANTHER: F[S]=91% F[F]=0% S1314F Disease 9 0.969 SNPs&GO S1314P Disease 7 0.859 PhD-SNP: F[S]=76% F[P]=0% Nali=602 S1314P Disease 9 0.970 PANTHER: F[S]=91% F[P]=0% S1314P Disease 9 0.966 SNPs&GO S1321F Disease 5 0.736 PhD-SNP: F[S]=38% F[F]=1% Nali=447 S1321F Neutral 1 0.442 PANTHER: F[S]=23% F[F]=1% S1321F Disease 9 0.949 SNPs&GO S1321Y Disease 4 0.704 PhD-SNP: F[S]=38% F[Y]=1% Nali=447 S1321Y Neutral 1 0.473 PANTHER: F[S]=23% F[Y]=1% S1321Y Disease 9 0.941 SNPs&GO F1327C Disease 7 0.870 PhD-SNP: F[F]=88% F[C]=0% Nali=518 F1327C Neutral 4 0.323 PANTHER: F[F]=6% F[C]=0% F1327C Disease 8 0.924 SNPs&GO I1373V Neutral 4 0.307 PhD-SNP: F[I]=38% F[V]=8% Nali=1097 I1373V Neutral 7 0.163 PANTHER: F[I]=51% F[V]=14% I1373V Disease 3 0.625 SNPs&GO L1387P Disease 8 0.908 PhD-SNP: F[L]=76% F[P]=0% Nali=1165 L1387P Disease 10 0.995 PANTHER: F[L]=95% F[P]=0% L1387P Disease 9 0.968 SNPs&GO E1392D Neutral 4 0.324 PhD-SNP: F[E]=18% F[D]=2% Nali=1168 E1392D Disease 5 0.734 PANTHER: F[E]=83% F[D]=2% E1392D Disease 9 0.958 SNPs&GO R1395Q Disease 6 0.780 PhD-SNP: F[R]=67% F[Q]=3% Nali=1183 R1395Q Disease 10 0.992 PANTHER: F[R]=97% F[Q]=0% R1395Q Disease 9 0.964 SNPs&GO R1395W Disease 8 0.920 PhD-SNP: F[R]=67% F[W]=0% Nali=1183 R1395W Disease 10 0.998 PANTHER: F[R]=97% F[W]=0% R1395W Disease 10 0.980 SNPs&GO Mutation: WT+POS+NEW WT: Residue in wild-type protein POS: Residue position NEW: New residue after mutation Prediction: Neutral: Neutral variation Disease: Disease associated variation RI: Reliability Index Probability: Disease probability (if >0.5 mutation is predicted Disease) Method: SVM type and data PANTHER: Output of the PANTHER algorithm PhD-SNP: SVM input is the sequence and profile at the mutated position SNPs&GO: SVM input is all the input in PhD-SNP, PANTHER and GO term features F[X]: Frequency of residue X in the sequence profile Nali: Number of aligned sequences in the mutated site ********************************************************************************************** ** ** ** Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. (2009). Functional ** ** annotations improve the predictive score of human disease-related mutations in ** ** proteins. Human Mutation. 30:1237-1244. ** ** ** ** Capriotti E, Altman RB. (2011). Improving the prediction of disease-related vari- ** ** ants using protein three-dimensional structure. BMC Bioinformatics. 12 (Sup.4) S3. ** ** ** **********************************************************************************************