********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: fileseq.seq Mutation Prediction RI Probability Method M22T Neutral 3 0.365 PhD-SNP: F[M]=6% F[T]=4% Nali=439 M22T Neutral 6 0.183 PANTHER: F[M]=10% F[T]=2% M22T Neutral 7 0.143 SNPs&GO P33R Disease 5 0.775 PhD-SNP: F[P]=96% F[R]=0% Nali=689 P33R Disease 10 0.986 PANTHER: F[P]=96% F[R]=0% P33R Disease 5 0.775 SNPs&GO P38S Neutral 1 0.464 PhD-SNP: F[P]=52% F[S]=6% Nali=715 P38S Disease 8 0.885 PANTHER: F[P]=90% F[S]=0% P38S Disease 3 0.627 SNPs&GO I53T Neutral 3 0.356 PhD-SNP: F[I]=19% F[T]=4% Nali=777 I53T Neutral 1 0.429 PANTHER: F[I]=38% F[T]=2% I53T Neutral 5 0.235 SNPs&GO R63H Neutral 1 0.449 PhD-SNP: F[R]=17% F[H]=1% Nali=885 R63H Neutral 0 0.488 PANTHER: F[R]=41% F[H]=2% R63H Neutral 3 0.368 SNPs&GO T69M Disease 3 0.632 PhD-SNP: F[T]=45% F[M]=1% Nali=898 T69M Disease 8 0.921 PANTHER: F[T]=77% F[M]=0% T69M Disease 4 0.720 SNPs&GO V79A Disease 5 0.747 PhD-SNP: F[V]=74% F[A]=0% Nali=911 V79A Neutral 1 0.429 PANTHER: F[V]=57% F[A]=3% V79A Disease 1 0.532 SNPs&GO R146W Disease 6 0.810 PhD-SNP: F[R]=38% F[W]=4% Nali=944 R146W Disease 7 0.841 PANTHER: F[R]=45% F[W]=0% R146W Disease 3 0.668 SNPs&GO R149S Neutral 1 0.428 PhD-SNP: F[R]=5% F[S]=2% Nali=947 R149S Disease 2 0.576 PANTHER: F[R]=65% F[S]=2% R149S Disease 1 0.528 SNPs&GO R186L Disease 0 0.522 PhD-SNP: F[R]=2% F[L]=0% Nali=972 R186L Neutral 4 0.319 PANTHER: F[R]=25% F[L]=2% R186L Neutral 4 0.296 SNPs&GO E276K Disease 1 0.560 PhD-SNP: F[E]=39% F[K]=5% Nali=942 E276K Neutral 1 0.470 PANTHER: F[E]=62% F[K]=3% E276K Disease 0 0.507 SNPs&GO I289M Disease 1 0.526 PhD-SNP: F[I]=13% F[M]=4% Nali=965 I289M Neutral 1 0.461 PANTHER: F[I]=47% F[M]=2% I289M Neutral 1 0.453 SNPs&GO A299V Disease 5 0.747 PhD-SNP: F[A]=90% F[V]=0% Nali=979 A299V Neutral 0 0.488 PANTHER: F[A]=62% F[V]=3% A299V Neutral 1 0.454 SNPs&GO E322K Disease 1 0.572 PhD-SNP: F[E]=6% F[K]=1% Nali=981 E322K Neutral 1 0.470 PANTHER: F[E]=62% F[K]=3% E322K Disease 3 0.663 SNPs&GO R337Q Disease 2 0.605 PhD-SNP: F[R]=72% F[Q]=9% Nali=939 R337Q Disease 1 0.529 PANTHER: F[R]=65% F[Q]=2% R337Q Disease 0 0.522 SNPs&GO M350I Disease 2 0.612 PhD-SNP: F[M]=8% F[I]=2% Nali=983 M350I Neutral 6 0.178 PANTHER: F[M]=32% F[I]=8% M350I Neutral 4 0.289 SNPs&GO A352S Disease 6 0.810 PhD-SNP: F[A]=97% F[S]=2% Nali=984 A352S Disease 4 0.725 PANTHER: F[A]=82% F[S]=3% A352S Disease 3 0.661 SNPs&GO A352V Disease 8 0.883 PhD-SNP: F[A]=97% F[V]=0% Nali=984 A352V Disease 7 0.841 PANTHER: F[A]=82% F[V]=1% A352V Disease 5 0.765 SNPs&GO P365S Disease 6 0.801 PhD-SNP: F[P]=94% F[S]=1% Nali=979 P365S Disease 10 0.981 PANTHER: F[P]=97% F[S]=0% P365S Disease 6 0.787 SNPs&GO R374Q Neutral 4 0.319 PhD-SNP: F[R]=25% F[Q]=11% Nali=981 R374Q Neutral 8 0.084 PANTHER: F[R]=28% F[Q]=20% R374Q Neutral 9 0.052 SNPs&GO V388L Neutral 6 0.203 PhD-SNP: F[V]=12% F[L]=5% Nali=971 V388L Neutral 4 0.299 PANTHER: F[V]=57% F[L]=7% V388L Neutral 5 0.253 SNPs&GO F409L Disease 4 0.696 PhD-SNP: F[F]=99% F[L]=0% Nali=968 F409L Disease 5 0.728 PANTHER: F[F]=82% F[L]=2% F409L Disease 2 0.600 SNPs&GO F427L Disease 3 0.648 PhD-SNP: F[F]=67% F[L]=11% Nali=964 F427L Disease 5 0.728 PANTHER: F[F]=82% F[L]=2% F427L Disease 3 0.640 SNPs&GO G439V Disease 8 0.902 PhD-SNP: F[G]=100% F[V]=0% Nali=947 G439V Disease 10 0.987 PANTHER: F[G]=96% F[V]=0% G439V Disease 7 0.836 SNPs&GO D468Y Disease 4 0.691 PhD-SNP: F[D]=35% F[Y]=0% Nali=732 D468Y Unclassified NA NA PANTHER: F[D]=NA F[Y]=NA D468Y Neutral 5 0.228 SNPs&GO D470N Disease 1 0.530 PhD-SNP: F[D]=55% F[N]=7% Nali=739 D470N Unclassified NA NA PANTHER: F[D]=NA F[N]=NA D470N Neutral 6 0.186 SNPs&GO F478V Disease 3 0.633 PhD-SNP: F[F]=38% F[V]=9% Nali=675 F478V Unclassified NA NA PANTHER: F[F]=NA F[V]=NA F478V Neutral 5 0.254 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. ** ** ** **********************************************************************************************