********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: SP.seq Mutation Prediction RI Probability Method E5K Neutral 3 0.356 PhD-SNP: F[E]=95% F[K]=0% Nali=18 E5K Unclassified NA NA PANTHER: F[E]=NA F[K]=NA E5K Neutral 8 0.081 SNPs&GO R26L Neutral 4 0.314 PhD-SNP: F[R]=48% F[L]=0% Nali=39 R26L Unclassified NA NA PANTHER: F[R]=NA F[L]=NA R26L Neutral 8 0.078 SNPs&GO P34R Neutral 9 0.055 PhD-SNP: F[P]=43% F[R]=2% Nali=52 P34R Unclassified NA NA PANTHER: F[P]=NA F[R]=NA P34R Neutral 10 0.022 SNPs&GO P55S Neutral 4 0.313 PhD-SNP: F[P]=42% F[S]=5% Nali=132 P55S Unclassified NA NA PANTHER: F[P]=NA F[S]=NA P55S Neutral 8 0.091 SNPs&GO R103Q Disease 3 0.669 PhD-SNP: F[R]=56% F[Q]=0% Nali=189 R103Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R103Q Neutral 4 0.280 SNPs&GO R127C Disease 6 0.787 PhD-SNP: F[R]=65% F[C]=0% Nali=191 R127C Unclassified NA NA PANTHER: F[R]=NA F[C]=NA R127C Neutral 3 0.334 SNPs&GO V140I Neutral 5 0.238 PhD-SNP: F[V]=26% F[I]=18% Nali=187 V140I Unclassified NA NA PANTHER: F[V]=NA F[I]=NA V140I Neutral 8 0.077 SNPs&GO I146V Neutral 3 0.367 PhD-SNP: F[I]=19% F[V]=2% Nali=191 I146V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I146V Neutral 7 0.146 SNPs&GO D151N Disease 4 0.702 PhD-SNP: F[D]=27% F[N]=7% Nali=180 D151N Unclassified NA NA PANTHER: F[D]=NA F[N]=NA D151N Neutral 5 0.274 SNPs&GO H154Q Neutral 5 0.250 PhD-SNP: F[H]=5% F[Q]=8% Nali=188 H154Q Unclassified NA NA PANTHER: F[H]=NA F[Q]=NA H154Q Neutral 8 0.089 SNPs&GO Y158C Disease 3 0.637 PhD-SNP: F[Y]=6% F[C]=0% Nali=191 Y158C Unclassified NA NA PANTHER: F[Y]=NA F[C]=NA Y158C Neutral 3 0.370 SNPs&GO S186G Neutral 3 0.364 PhD-SNP: F[S]=41% F[G]=5% Nali=195 S186G Unclassified NA NA PANTHER: F[S]=NA F[G]=NA S186G Neutral 8 0.116 SNPs&GO Q220R Neutral 8 0.116 PhD-SNP: F[Q]=13% F[R]=4% Nali=131 Q220R Unclassified NA NA PANTHER: F[Q]=NA F[R]=NA Q220R Neutral 8 0.075 SNPs&GO T223M Neutral 8 0.114 PhD-SNP: F[T]=32% F[M]=0% Nali=122 T223M Unclassified NA NA PANTHER: F[T]=NA F[M]=NA T223M Neutral 9 0.038 SNPs&GO H243R Neutral 8 0.079 PhD-SNP: F[H]=24% F[R]=4% Nali=123 H243R Unclassified NA NA PANTHER: F[H]=NA F[R]=NA H243R Neutral 9 0.029 SNPs&GO T251M Neutral 6 0.213 PhD-SNP: F[T]=33% F[M]=2% Nali=131 T251M Unclassified NA NA PANTHER: F[T]=NA F[M]=NA T251M Neutral 9 0.072 SNPs&GO V263A Neutral 8 0.083 PhD-SNP: F[V]=13% F[A]=23% Nali=183 V263A Unclassified NA NA PANTHER: F[V]=NA F[A]=NA V263A Neutral 9 0.037 SNPs&GO Y266C Disease 1 0.572 PhD-SNP: F[Y]=34% F[C]=1% Nali=178 Y266C Unclassified NA NA PANTHER: F[Y]=NA F[C]=NA Y266C Neutral 3 0.367 SNPs&GO V277M Neutral 1 0.444 PhD-SNP: F[V]=51% F[M]=0% Nali=182 V277M Unclassified NA NA PANTHER: F[V]=NA F[M]=NA V277M Neutral 7 0.137 SNPs&GO R299Q Neutral 1 0.425 PhD-SNP: F[R]=26% F[Q]=3% Nali=173 R299Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R299Q Neutral 6 0.197 SNPs&GO G305S Neutral 2 0.389 PhD-SNP: F[G]=24% F[S]=3% Nali=183 G305S Unclassified NA NA PANTHER: F[G]=NA F[S]=NA G305S Neutral 8 0.120 SNPs&GO I311T Neutral 4 0.318 PhD-SNP: F[I]=29% F[T]=8% Nali=181 I311T Unclassified NA NA PANTHER: F[I]=NA F[T]=NA I311T Neutral 9 0.070 SNPs&GO M350V Neutral 6 0.191 PhD-SNP: F[M]=21% F[V]=7% Nali=182 M350V Unclassified NA NA PANTHER: F[M]=NA F[V]=NA M350V Neutral 9 0.072 SNPs&GO I357T Neutral 4 0.284 PhD-SNP: F[I]=34% F[T]=9% Nali=179 I357T Unclassified NA NA PANTHER: F[I]=NA F[T]=NA I357T Neutral 9 0.068 SNPs&GO R366Q Disease 6 0.785 PhD-SNP: F[R]=56% F[Q]=1% Nali=179 R366Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R366Q Neutral 2 0.380 SNPs&GO L389V Neutral 5 0.275 PhD-SNP: F[L]=47% F[V]=9% Nali=172 L389V Unclassified NA NA PANTHER: F[L]=NA F[V]=NA L389V Neutral 8 0.113 SNPs&GO A399E Disease 1 0.552 PhD-SNP: F[A]=17% F[E]=0% Nali=179 A399E Unclassified NA NA PANTHER: F[A]=NA F[E]=NA A399E Neutral 3 0.366 SNPs&GO A404D Disease 8 0.882 PhD-SNP: F[A]=42% F[D]=1% Nali=177 A404D Unclassified NA NA PANTHER: F[A]=NA F[D]=NA A404D Disease 4 0.675 SNPs&GO P415H Disease 5 0.767 PhD-SNP: F[P]=69% F[H]=0% Nali=175 P415H Unclassified NA NA PANTHER: F[P]=NA F[H]=NA P415H Neutral 6 0.207 SNPs&GO A466S Neutral 6 0.201 PhD-SNP: F[A]=46% F[S]=13% Nali=173 A466S Unclassified NA NA PANTHER: F[A]=NA F[S]=NA A466S Neutral 9 0.058 SNPs&GO G467R Disease 6 0.815 PhD-SNP: F[G]=94% F[R]=0% Nali=173 G467R Unclassified NA NA PANTHER: F[G]=NA F[R]=NA G467R Neutral 2 0.382 SNPs&GO R471H Neutral 6 0.180 PhD-SNP: F[R]=15% F[H]=1% Nali=167 R471H Unclassified NA NA PANTHER: F[R]=NA F[H]=NA R471H Neutral 8 0.076 SNPs&GO R478H Neutral 8 0.107 PhD-SNP: F[R]=4% F[H]=1% Nali=169 R478H Unclassified NA NA PANTHER: F[R]=NA F[H]=NA R478H Neutral 9 0.051 SNPs&GO R478S Neutral 9 0.059 PhD-SNP: F[R]=4% F[S]=30% Nali=169 R478S Unclassified NA NA PANTHER: F[R]=NA F[S]=NA R478S Neutral 10 0.023 SNPs&GO K480R Neutral 8 0.089 PhD-SNP: F[K]=8% F[R]=2% Nali=166 K480R Unclassified NA NA PANTHER: F[K]=NA F[R]=NA K480R Neutral 9 0.045 SNPs&GO D524E Neutral 9 0.029 PhD-SNP: F[D]=19% F[E]=19% Nali=92 D524E Unclassified NA NA PANTHER: F[D]=NA F[E]=NA D524E Neutral 10 0.010 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. ** ** ** **********************************************************************************************