********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: SP.seq Mutation Prediction RI Probability Method I259M Neutral 9 0.074 PhD-SNP: F[I]=43% F[M]=0% Nali=43 I259M Neutral 8 0.120 PANTHER: F[I]=9% F[M]=5% I259M Neutral 10 0.015 SNPs&GO S260G Neutral 9 0.056 PhD-SNP: F[S]=59% F[G]=12% Nali=40 S260G Neutral 5 0.248 PANTHER: F[S]=22% F[G]=4% S260G Neutral 10 0.011 SNPs&GO S260N Neutral 9 0.051 PhD-SNP: F[S]=59% F[N]=12% Nali=40 S260N Neutral 3 0.354 PANTHER: F[S]=22% F[N]=2% S260N Neutral 10 0.021 SNPs&GO M262L Neutral 9 0.039 PhD-SNP: F[M]=20% F[L]=29% Nali=44 M262L Neutral 8 0.103 PANTHER: F[M]=9% F[L]=7% M262L Neutral 10 0.013 SNPs&GO M262T Neutral 8 0.101 PhD-SNP: F[M]=20% F[T]=0% Nali=44 M262T Neutral 7 0.132 PANTHER: F[M]=9% F[T]=5% M262T Neutral 9 0.029 SNPs&GO K265E Neutral 2 0.401 PhD-SNP: F[K]=79% F[E]=6% Nali=47 K265E Neutral 7 0.136 PANTHER: F[K]=21% F[E]=10% K265E Neutral 9 0.063 SNPs&GO E267K Disease 1 0.532 PhD-SNP: F[E]=83% F[K]=0% Nali=46 E267K Neutral 6 0.212 PANTHER: F[E]=24% F[K]=6% E267K Neutral 7 0.153 SNPs&GO E267Q Neutral 3 0.356 PhD-SNP: F[E]=83% F[Q]=2% Nali=46 E267Q Neutral 5 0.263 PANTHER: F[E]=24% F[Q]=4% E267Q Neutral 8 0.083 SNPs&GO P268R Neutral 5 0.272 PhD-SNP: F[P]=66% F[R]=6% Nali=46 P268R Neutral 6 0.210 PANTHER: F[P]=16% F[R]=4% P268R Neutral 9 0.046 SNPs&GO F269L Neutral 9 0.057 PhD-SNP: F[F]=33% F[L]=29% Nali=47 F269L Neutral 8 0.100 PANTHER: F[F]=15% F[L]=20% F269L Neutral 10 0.018 SNPs&GO D271E Neutral 9 0.050 PhD-SNP: F[D]=54% F[E]=33% Nali=45 D271E Neutral 8 0.124 PANTHER: F[D]=18% F[E]=10% D271E Neutral 10 0.009 SNPs&GO L273P Neutral 2 0.408 PhD-SNP: F[L]=54% F[P]=10% Nali=40 L273P Unclassified NA NA PANTHER: F[L]=NA F[P]=NA L273P Neutral 8 0.106 SNPs&GO L273R Neutral 0 0.493 PhD-SNP: F[L]=54% F[R]=5% Nali=40 L273R Unclassified NA NA PANTHER: F[L]=NA F[R]=NA L273R Neutral 8 0.100 SNPs&GO F274L Neutral 8 0.089 PhD-SNP: F[F]=40% F[L]=17% Nali=41 F274L Unclassified NA NA PANTHER: F[F]=NA F[L]=NA F274L Neutral 10 0.022 SNPs&GO P275L Neutral 6 0.194 PhD-SNP: F[P]=67% F[L]=2% Nali=41 P275L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P275L Neutral 9 0.034 SNPs&GO A276T Neutral 8 0.099 PhD-SNP: F[A]=39% F[T]=2% Nali=43 A276T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A276T Neutral 10 0.024 SNPs&GO S278T Neutral 9 0.067 PhD-SNP: F[S]=45% F[T]=7% Nali=41 S278T Unclassified NA NA PANTHER: F[S]=NA F[T]=NA S278T Neutral 10 0.016 SNPs&GO P280L Neutral 7 0.139 PhD-SNP: F[P]=47% F[L]=0% Nali=44 P280L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P280L Neutral 9 0.034 SNPs&GO P280T Neutral 8 0.082 PhD-SNP: F[P]=47% F[T]=2% Nali=44 P280T Unclassified NA NA PANTHER: F[P]=NA F[T]=NA P280T Neutral 10 0.016 SNPs&GO S281G Neutral 9 0.057 PhD-SNP: F[S]=38% F[G]=16% Nali=44 S281G Unclassified NA NA PANTHER: F[S]=NA F[G]=NA S281G Neutral 10 0.018 SNPs&GO S281N Neutral 8 0.113 PhD-SNP: F[S]=38% F[N]=0% Nali=44 S281N Unclassified NA NA PANTHER: F[S]=NA F[N]=NA S281N Neutral 9 0.040 SNPs&GO G282S Neutral 9 0.051 PhD-SNP: F[G]=37% F[S]=11% Nali=45 G282S Unclassified NA NA PANTHER: F[G]=NA F[S]=NA G282S Neutral 10 0.012 SNPs&GO E284K Neutral 9 0.062 PhD-SNP: F[E]=52% F[K]=22% Nali=45 E284K Unclassified NA NA PANTHER: F[E]=NA F[K]=NA E284K Neutral 10 0.014 SNPs&GO E284Q Neutral 8 0.095 PhD-SNP: F[E]=52% F[Q]=4% Nali=45 E284Q Unclassified NA NA PANTHER: F[E]=NA F[Q]=NA E284Q Neutral 10 0.022 SNPs&GO T285A Neutral 9 0.036 PhD-SNP: F[T]=41% F[A]=20% Nali=45 T285A Unclassified NA NA PANTHER: F[T]=NA F[A]=NA T285A Neutral 10 0.013 SNPs&GO A286D Neutral 5 0.229 PhD-SNP: F[A]=49% F[D]=4% Nali=44 A286D Unclassified NA NA PANTHER: F[A]=NA F[D]=NA A286D Neutral 9 0.061 SNPs&GO A286V Neutral 8 0.085 PhD-SNP: F[A]=49% F[V]=0% Nali=44 A286V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A286V Neutral 10 0.021 SNPs&GO R287C Neutral 4 0.299 PhD-SNP: F[R]=67% F[C]=0% Nali=44 R287C Disease 5 0.761 PANTHER: F[R]=39% F[C]=0% R287C Neutral 5 0.242 SNPs&GO R287H Neutral 6 0.211 PhD-SNP: F[R]=67% F[H]=2% Nali=44 R287H Disease 1 0.560 PANTHER: F[R]=39% F[H]=1% R287H Neutral 7 0.135 SNPs&GO V289M Neutral 6 0.207 PhD-SNP: F[V]=83% F[M]=0% Nali=45 V289M Disease 3 0.665 PANTHER: F[V]=62% F[M]=1% V289M Neutral 6 0.209 SNPs&GO M292T Neutral 6 0.193 PhD-SNP: F[M]=18% F[T]=0% Nali=43 M292T Neutral 4 0.302 PANTHER: F[M]=17% F[T]=2% M292T Neutral 8 0.109 SNPs&GO L294P Disease 6 0.790 PhD-SNP: F[L]=68% F[P]=0% Nali=43 L294P Disease 7 0.856 PANTHER: F[L]=70% F[P]=0% L294P Disease 5 0.760 SNPs&GO S295C Neutral 3 0.350 PhD-SNP: F[S]=50% F[C]=0% Nali=43 S295C Disease 3 0.672 PANTHER: F[S]=26% F[C]=0% S295C Neutral 6 0.219 SNPs&GO G296A Neutral 4 0.325 PhD-SNP: F[G]=55% F[A]=0% Nali=43 G296A Neutral 5 0.255 PANTHER: F[G]=32% F[A]=6% G296A Neutral 8 0.094 SNPs&GO F298S Disease 2 0.617 PhD-SNP: F[F]=48% F[S]=2% Nali=43 F298S Disease 2 0.578 PANTHER: F[F]=28% F[S]=1% F298S Disease 2 0.616 SNPs&GO Y299C Neutral 0 0.497 PhD-SNP: F[Y]=68% F[C]=5% Nali=43 Y299C Neutral 5 0.245 PANTHER: F[Y]=25% F[C]=5% Y299C Neutral 8 0.104 SNPs&GO A300V Neutral 6 0.181 PhD-SNP: F[A]=31% F[V]=2% Nali=41 A300V Neutral 8 0.121 PANTHER: F[A]=21% F[V]=12% A300V Neutral 9 0.043 SNPs&GO A301S Neutral 9 0.033 PhD-SNP: F[A]=29% F[S]=44% Nali=40 A301S Neutral 8 0.099 PANTHER: F[A]=17% F[S]=23% A301S Neutral 10 0.016 SNPs&GO A301T Neutral 8 0.112 PhD-SNP: F[A]=29% F[T]=10% Nali=40 A301T Neutral 6 0.209 PANTHER: F[A]=17% F[T]=4% A301T Neutral 9 0.042 SNPs&GO D302E Neutral 7 0.133 PhD-SNP: F[D]=67% F[E]=22% Nali=35 D302E Neutral 6 0.181 PANTHER: F[D]=49% F[E]=16% D302E Neutral 9 0.037 SNPs&GO W303R Disease 3 0.652 PhD-SNP: F[W]=72% F[R]=0% Nali=35 W303R Disease 7 0.835 PANTHER: F[W]=81% F[R]=0% W303R Disease 4 0.679 SNPs&GO L306Q Disease 3 0.657 PhD-SNP: F[L]=86% F[Q]=0% Nali=41 L306Q Disease 6 0.825 PANTHER: F[L]=70% F[Q]=0% L306Q Disease 3 0.639 SNPs&GO S308G Neutral 7 0.126 PhD-SNP: F[S]=32% F[G]=10% Nali=40 S308G Neutral 8 0.122 PANTHER: F[S]=11% F[G]=6% S308G 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. ** ** ** **********************************************************************************************