********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: SP.seq Mutation Prediction RI Probability Method S42T Neutral 7 0.147 PhD-SNP: F[S]=51% F[T]=7% Nali=125 S42T Unclassified NA NA PANTHER: F[S]=NA F[T]=NA S42T Neutral 9 0.026 SNPs&GO K46R Neutral 1 0.430 PhD-SNP: F[K]=83% F[R]=6% Nali=132 K46R Unclassified NA NA PANTHER: F[K]=NA F[R]=NA K46R Neutral 8 0.108 SNPs&GO I97M Neutral 6 0.217 PhD-SNP: F[I]=23% F[M]=4% Nali=176 I97M Unclassified NA NA PANTHER: F[I]=NA F[M]=NA I97M Neutral 8 0.080 SNPs&GO V113M Neutral 6 0.201 PhD-SNP: F[V]=40% F[M]=17% Nali=192 V113M Unclassified NA NA PANTHER: F[V]=NA F[M]=NA V113M Neutral 9 0.039 SNPs&GO F148L Disease 2 0.619 PhD-SNP: F[F]=35% F[L]=5% Nali=189 F148L Unclassified NA NA PANTHER: F[F]=NA F[L]=NA F148L Neutral 5 0.244 SNPs&GO M170T Neutral 5 0.252 PhD-SNP: F[M]=6% F[T]=2% Nali=191 M170T Unclassified NA NA PANTHER: F[M]=NA F[T]=NA M170T Neutral 7 0.147 SNPs&GO Y198C Disease 3 0.640 PhD-SNP: F[Y]=42% F[C]=0% Nali=196 Y198C Unclassified NA NA PANTHER: F[Y]=NA F[C]=NA Y198C Neutral 4 0.290 SNPs&GO S238N Neutral 9 0.061 PhD-SNP: F[S]=23% F[N]=7% Nali=114 S238N Unclassified NA NA PANTHER: F[S]=NA F[N]=NA S238N Neutral 10 0.017 SNPs&GO E250K Neutral 4 0.322 PhD-SNP: F[E]=26% F[K]=3% Nali=121 E250K Unclassified NA NA PANTHER: F[E]=NA F[K]=NA E250K Neutral 8 0.101 SNPs&GO L256M Neutral 8 0.107 PhD-SNP: F[L]=40% F[M]=21% Nali=171 L256M Unclassified NA NA PANTHER: F[L]=NA F[M]=NA L256M Neutral 9 0.033 SNPs&GO P283L Neutral 6 0.185 PhD-SNP: F[P]=43% F[L]=2% Nali=168 P283L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P283L Neutral 9 0.064 SNPs&GO A286G Neutral 8 0.109 PhD-SNP: F[A]=19% F[G]=4% Nali=184 A286G Unclassified NA NA PANTHER: F[A]=NA F[G]=NA A286G Neutral 9 0.055 SNPs&GO I349V Neutral 9 0.039 PhD-SNP: F[I]=27% F[V]=25% Nali=181 I349V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I349V Neutral 10 0.014 SNPs&GO Y444C Disease 3 0.655 PhD-SNP: F[Y]=39% F[C]=1% Nali=175 Y444C Unclassified NA NA PANTHER: F[Y]=NA F[C]=NA Y444C Neutral 5 0.266 SNPs&GO T470S Neutral 8 0.110 PhD-SNP: F[T]=27% F[S]=14% Nali=171 T470S Unclassified NA NA PANTHER: F[T]=NA F[S]=NA T470S Neutral 9 0.037 SNPs&GO G472A Neutral 8 0.092 PhD-SNP: F[G]=30% F[A]=24% Nali=168 G472A Unclassified NA NA PANTHER: F[G]=NA F[A]=NA G472A Neutral 9 0.026 SNPs&GO S474L Neutral 5 0.227 PhD-SNP: F[S]=17% F[L]=3% Nali=168 S474L Unclassified NA NA PANTHER: F[S]=NA F[L]=NA S474L Neutral 8 0.076 SNPs&GO M504I Neutral 7 0.150 PhD-SNP: F[M]=4% F[I]=6% Nali=160 M504I Unclassified NA NA PANTHER: F[M]=NA F[I]=NA M504I Neutral 8 0.081 SNPs&GO R512W Neutral 2 0.404 PhD-SNP: F[R]=30% F[W]=0% Nali=144 R512W Unclassified NA NA PANTHER: F[R]=NA F[W]=NA R512W Neutral 7 0.159 SNPs&GO A518T Neutral 8 0.081 PhD-SNP: F[A]=28% F[T]=1% Nali=137 A518T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A518T Neutral 9 0.026 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. ** ** ** **********************************************************************************************