********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: SP.seq Mutation Prediction RI Probability Method V22M Neutral 8 0.101 PhD-SNP: F[V]=22% F[M]=32% Nali=601 V22M Disease 3 0.628 PANTHER: F[V]=49% F[M]=2% V22M Neutral 5 0.269 SNPs&GO G43R Disease 2 0.576 PhD-SNP: F[G]=38% F[R]=2% Nali=967 G43R Neutral 8 0.107 PANTHER: F[G]=25% F[R]=20% G43R Neutral 7 0.165 SNPs&GO T68P Disease 8 0.889 PhD-SNP: F[T]=38% F[P]=0% Nali=954 T68P Disease 1 0.548 PANTHER: F[T]=27% F[P]=1% T68P Disease 6 0.783 SNPs&GO I69V Neutral 8 0.106 PhD-SNP: F[I]=17% F[V]=42% Nali=962 I69V Neutral 6 0.186 PANTHER: F[I]=54% F[V]=21% I69V Neutral 7 0.156 SNPs&GO Y90C Disease 4 0.704 PhD-SNP: F[Y]=2% F[C]=0% Nali=996 Y90C Disease 7 0.832 PANTHER: F[Y]=31% F[C]=0% Y90C Disease 6 0.781 SNPs&GO V96L Disease 1 0.568 PhD-SNP: F[V]=69% F[L]=6% Nali=996 V96L Neutral 5 0.232 PANTHER: F[V]=49% F[L]=14% V96L Neutral 3 0.371 SNPs&GO T107A Neutral 8 0.091 PhD-SNP: F[T]=10% F[A]=50% Nali=996 T107A Neutral 5 0.241 PANTHER: F[T]=23% F[A]=6% T107A Neutral 8 0.121 SNPs&GO V127M Disease 4 0.699 PhD-SNP: F[V]=60% F[M]=1% Nali=986 V127M Disease 1 0.528 PANTHER: F[V]=42% F[M]=2% V127M Neutral 0 0.493 SNPs&GO N154S Neutral 7 0.144 PhD-SNP: F[N]=25% F[S]=9% Nali=804 N154S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N154S Neutral 8 0.101 SNPs&GO H156Y Neutral 5 0.266 PhD-SNP: F[H]=23% F[Y]=3% Nali=785 H156Y Neutral 8 0.091 PANTHER: F[H]=2% F[Y]=1% H156Y Neutral 9 0.043 SNPs&GO C160Y Disease 4 0.683 PhD-SNP: F[C]=18% F[Y]=4% Nali=682 C160Y Disease 8 0.877 PANTHER: F[C]=79% F[Y]=0% C160Y Disease 7 0.843 SNPs&GO K180E Disease 0 0.516 PhD-SNP: F[K]=15% F[E]=6% Nali=622 K180E Unclassified NA NA PANTHER: F[K]=NA F[E]=NA K180E Neutral 5 0.275 SNPs&GO Y184C Disease 1 0.568 PhD-SNP: F[Y]=2% F[C]=0% Nali=591 Y184C Unclassified NA NA PANTHER: F[Y]=NA F[C]=NA Y184C Neutral 3 0.374 SNPs&GO R200H Disease 3 0.664 PhD-SNP: F[R]=84% F[H]=2% Nali=63 R200H Unclassified NA NA PANTHER: F[R]=NA F[H]=NA R200H Neutral 1 0.463 SNPs&GO R209C Neutral 0 0.478 PhD-SNP: F[R]=38% F[C]=0% Nali=49 R209C Unclassified NA NA PANTHER: F[R]=NA F[C]=NA R209C Neutral 4 0.320 SNPs&GO A210V Neutral 4 0.309 PhD-SNP: F[A]=55% F[V]=0% Nali=50 A210V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A210V Neutral 6 0.206 SNPs&GO E228K Disease 0 0.501 PhD-SNP: F[E]=76% F[K]=3% Nali=32 E228K Unclassified NA NA PANTHER: F[E]=NA F[K]=NA E228K Neutral 4 0.295 SNPs&GO N233K Neutral 9 0.063 PhD-SNP: F[N]=19% F[K]=16% Nali=30 N233K Unclassified NA NA PANTHER: F[N]=NA F[K]=NA N233K Neutral 9 0.067 SNPs&GO A238T Neutral 2 0.405 PhD-SNP: F[A]=70% F[T]=7% Nali=29 A238T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A238T Neutral 7 0.156 SNPs&GO D241N Neutral 4 0.297 PhD-SNP: F[D]=33% F[N]=4% Nali=26 D241N Unclassified NA NA PANTHER: F[D]=NA F[N]=NA D241N Neutral 7 0.130 SNPs&GO P256T Disease 3 0.657 PhD-SNP: F[P]=92% F[T]=0% Nali=24 P256T Unclassified NA NA PANTHER: F[P]=NA F[T]=NA P256T Neutral 4 0.302 SNPs&GO K275E Disease 2 0.602 PhD-SNP: F[K]=80% F[E]=0% Nali=19 K275E Unclassified NA NA PANTHER: F[K]=NA F[E]=NA K275E Neutral 2 0.390 SNPs&GO Q278H Neutral 2 0.387 PhD-SNP: F[Q]=63% F[H]=0% Nali=18 Q278H Unclassified NA NA PANTHER: F[Q]=NA F[H]=NA Q278H Neutral 7 0.142 SNPs&GO Q309R Disease 2 0.603 PhD-SNP: F[Q]=58% F[R]=0% Nali=18 Q309R Unclassified NA NA PANTHER: F[Q]=NA F[R]=NA Q309R Neutral 4 0.290 SNPs&GO V317I Neutral 3 0.363 PhD-SNP: F[V]=53% F[I]=6% Nali=16 V317I Unclassified NA NA PANTHER: F[V]=NA F[I]=NA V317I Neutral 7 0.165 SNPs&GO K321E Disease 1 0.564 PhD-SNP: F[K]=42% F[E]=5% Nali=18 K321E Unclassified NA NA PANTHER: F[K]=NA F[E]=NA K321E Neutral 3 0.367 SNPs&GO E340D Neutral 7 0.158 PhD-SNP: F[E]=53% F[D]=12% Nali=16 E340D Unclassified NA NA PANTHER: F[E]=NA F[D]=NA E340D Neutral 9 0.070 SNPs&GO P378T Neutral 6 0.184 PhD-SNP: F[P]=68% F[T]=0% Nali=18 P378T Unclassified NA NA PANTHER: F[P]=NA F[T]=NA P378T Neutral 9 0.026 SNPs&GO P386S Neutral 7 0.135 PhD-SNP: F[P]=58% F[S]=16% Nali=18 P386S Unclassified NA NA PANTHER: F[P]=NA F[S]=NA P386S Neutral 9 0.037 SNPs&GO K387E Neutral 1 0.449 PhD-SNP: F[K]=79% F[E]=0% Nali=18 K387E Unclassified NA NA PANTHER: F[K]=NA F[E]=NA K387E Neutral 7 0.171 SNPs&GO N403K Neutral 0 0.483 PhD-SNP: F[N]=53% F[K]=0% Nali=18 N403K Unclassified NA NA PANTHER: F[N]=NA F[K]=NA N403K Neutral 5 0.258 SNPs&GO Q417P Neutral 0 0.480 PhD-SNP: F[Q]=79% F[P]=5% Nali=18 Q417P Unclassified NA NA PANTHER: F[Q]=NA F[P]=NA Q417P Neutral 7 0.165 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. ** ** ** **********************************************************************************************