********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** WARNING: Incorrect mutation N2091D WARNING: Incorrect mutation N2091S WARNING: Incorrect mutation N2091K WARNING: Incorrect mutation G2092D WARNING: Incorrect mutation G2092A WARNING: Incorrect mutation A2093S WARNING: Incorrect mutation A2093G WARNING: Incorrect mutation L2094F WARNING: Incorrect mutation L2095F WARNING: Incorrect mutation F2097I WARNING: Incorrect mutation F2097S WARNING: Incorrect mutation V2098M WARNING: Incorrect mutation V2098G WARNING: Incorrect mutation R2101K WARNING: Incorrect mutation D2102E WARNING: Incorrect mutation A2103T WARNING: Incorrect mutation A2103S WARNING: Incorrect mutation A2103V WARNING: Incorrect mutation G2104R WARNING: Incorrect mutation D2106E WARNING: Incorrect mutation R2107Q WARNING: Incorrect mutation R2107P WARNING: Incorrect mutation R2107L WARNING: Incorrect mutation A2108T WARNING: Incorrect mutation A2108V WARNING: Incorrect mutation G2110S WARNING: Incorrect mutation G2110C WARNING: Incorrect mutation G2110D WARNING: Incorrect mutation G2110V WARNING: Incorrect mutation E2111K WARNING: Incorrect mutation E2112Q WARNING: Incorrect mutation E2112D WARNING: Incorrect mutation D2113N WARNING: Incorrect mutation D2113A WARNING: Incorrect mutation A2114P WARNING: Incorrect mutation G2115C WARNING: Incorrect mutation G2115D WARNING: Incorrect mutation G2115A WARNING: Incorrect mutation C2116F WARNING: Incorrect mutation V2117A WARNING: Incorrect mutation V2117G WARNING: Incorrect mutation R2118S WARNING: Incorrect mutation R2118C WARNING: Incorrect mutation R2118H WARNING: Incorrect mutation A2119T WARNING: Incorrect mutation A2119E WARNING: Incorrect mutation R2120W WARNING: Incorrect mutation R2120Q WARNING: Incorrect mutation R2120L WARNING: Incorrect mutation G2121S WARNING: Incorrect mutation G2121D WARNING: Incorrect mutation R2122Q WARNING: Incorrect mutation P2123R WARNING: Incorrect mutation P2123L WARNING: Incorrect mutation S2124N WARNING: Incorrect mutation E2125G WARNING: Incorrect mutation E2126G WARNING: Incorrect mutation L2128I WARNING: Incorrect mutation Q2129R WARNING: Incorrect mutation D2130N WARNING: Incorrect mutation D2130Y WARNING: Incorrect mutation S2131G WARNING: Incorrect mutation S2131I WARNING: Incorrect mutation S2131R WARNING: Incorrect mutation R2132G WARNING: Incorrect mutation V2133F WARNING: Incorrect mutation V2135I WARNING: Incorrect mutation V2135F WARNING: Incorrect mutation S2136N Sequence File: CAC1C_HUMAN.seq Mutation Prediction RI Probability Method P2096H Disease 1 0.569 PhD-SNP: F[P]=90% F[H]=0% Nali=82 P2096H Neutral 0 0.482 PANTHER: F[P]=30% F[H]=1% P2096H Disease 8 0.897 SNPs&GO P2096S Disease 1 0.564 PhD-SNP: F[P]=90% F[S]=1% Nali=82 P2096S Neutral 7 0.174 PANTHER: F[P]=30% F[S]=6% P2096S Disease 8 0.878 SNPs&GO G2109R Neutral 1 0.463 PhD-SNP: F[G]=33% F[R]=0% Nali=90 G2109R Disease 0 0.510 PANTHER: F[G]=63% F[R]=1% G2109R Disease 9 0.959 SNPs&GO G2109V Neutral 2 0.421 PhD-SNP: F[G]=33% F[V]=0% Nali=90 G2109V Neutral 0 0.476 PANTHER: F[G]=63% F[V]=2% G2109V Disease 9 0.938 SNPs&GO E2127D Disease 3 0.665 PhD-SNP: F[E]=96% F[D]=0% Nali=91 E2127D Unclassified NA NA PANTHER: F[E]=NA F[D]=NA E2127D Disease 8 0.917 SNPs&GO E2127Q Disease 3 0.653 PhD-SNP: F[E]=96% F[Q]=0% Nali=91 E2127Q Unclassified NA NA PANTHER: F[E]=NA F[Q]=NA E2127Q Disease 8 0.890 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. ** ** ** **********************************************************************************************