********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: SP.seq Mutation Prediction RI Probability Method M1I Neutral 8 0.093 PhD-SNP: F[M]=95% F[I]=0% Nali=18 M1I Unclassified NA NA PANTHER: F[M]=NA F[I]=NA M1I Neutral 9 0.046 SNPs&GO A7T Neutral 6 0.183 PhD-SNP: F[A]=65% F[T]=0% Nali=19 A7T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A7T Neutral 9 0.034 SNPs&GO E8Q Neutral 2 0.390 PhD-SNP: F[E]=95% F[Q]=0% Nali=19 E8Q Unclassified NA NA PANTHER: F[E]=NA F[Q]=NA E8Q Neutral 8 0.095 SNPs&GO S11Y Neutral 0 0.492 PhD-SNP: F[S]=81% F[Y]=0% Nali=20 S11Y Unclassified NA NA PANTHER: F[S]=NA F[Y]=NA S11Y Neutral 8 0.079 SNPs&GO A13V Neutral 4 0.314 PhD-SNP: F[A]=79% F[V]=0% Nali=18 A13V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A13V Neutral 9 0.053 SNPs&GO P17R Neutral 4 0.279 PhD-SNP: F[P]=62% F[R]=0% Nali=20 P17R Unclassified NA NA PANTHER: F[P]=NA F[R]=NA P17R Neutral 9 0.055 SNPs&GO Q29P Neutral 7 0.153 PhD-SNP: F[Q]=30% F[P]=7% Nali=43 Q29P Unclassified NA NA PANTHER: F[Q]=NA F[P]=NA Q29P Neutral 9 0.039 SNPs&GO A50E Disease 6 0.789 PhD-SNP: F[A]=40% F[E]=0% Nali=140 A50E Unclassified NA NA PANTHER: F[A]=NA F[E]=NA A50E Neutral 3 0.350 SNPs&GO A54G Neutral 2 0.381 PhD-SNP: F[A]=30% F[G]=1% Nali=133 A54G Unclassified NA NA PANTHER: F[A]=NA F[G]=NA A54G Neutral 8 0.105 SNPs&GO T59M Neutral 2 0.415 PhD-SNP: F[T]=45% F[M]=2% Nali=139 T59M Unclassified NA NA PANTHER: F[T]=NA F[M]=NA T59M Neutral 8 0.115 SNPs&GO V74E Disease 8 0.894 PhD-SNP: F[V]=78% F[E]=0% Nali=129 V74E Unclassified NA NA PANTHER: F[V]=NA F[E]=NA V74E Disease 1 0.537 SNPs&GO A107T Disease 6 0.787 PhD-SNP: F[A]=77% F[T]=0% Nali=191 A107T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A107T Neutral 4 0.286 SNPs&GO P111L Disease 6 0.780 PhD-SNP: F[P]=82% F[L]=2% Nali=192 P111L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P111L Neutral 5 0.253 SNPs&GO T123S Neutral 6 0.190 PhD-SNP: F[T]=62% F[S]=18% Nali=167 T123S Unclassified NA NA PANTHER: F[T]=NA F[S]=NA T123S Neutral 9 0.045 SNPs&GO C124F Disease 1 0.561 PhD-SNP: F[C]=4% F[F]=1% Nali=167 C124F Unclassified NA NA PANTHER: F[C]=NA F[F]=NA C124F Neutral 5 0.227 SNPs&GO V149M Disease 2 0.589 PhD-SNP: F[V]=49% F[M]=2% Nali=189 V149M Unclassified NA NA PANTHER: F[V]=NA F[M]=NA V149M Neutral 7 0.150 SNPs&GO P150H Disease 9 0.948 PhD-SNP: F[P]=89% F[H]=0% Nali=188 P150H Unclassified NA NA PANTHER: F[P]=NA F[H]=NA P150H Disease 1 0.568 SNPs&GO G155S Disease 4 0.722 PhD-SNP: F[G]=52% F[S]=6% Nali=190 G155S Unclassified NA NA PANTHER: F[G]=NA F[S]=NA G155S Neutral 3 0.341 SNPs&GO H175Y Neutral 2 0.424 PhD-SNP: F[H]=21% F[Y]=2% Nali=192 H175Y Unclassified NA NA PANTHER: F[H]=NA F[Y]=NA H175Y Neutral 6 0.203 SNPs&GO G215R Disease 4 0.694 PhD-SNP: F[G]=60% F[R]=0% Nali=165 G215R Unclassified NA NA PANTHER: F[G]=NA F[R]=NA G215R Neutral 4 0.306 SNPs&GO Q220K Neutral 7 0.152 PhD-SNP: F[Q]=13% F[K]=5% Nali=131 Q220K Unclassified NA NA PANTHER: F[Q]=NA F[K]=NA Q220K Neutral 8 0.099 SNPs&GO A221V Neutral 6 0.181 PhD-SNP: F[A]=44% F[V]=11% Nali=130 A221V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A221V Neutral 9 0.054 SNPs&GO V234A Neutral 6 0.203 PhD-SNP: F[V]=45% F[A]=1% Nali=111 V234A Unclassified NA NA PANTHER: F[V]=NA F[A]=NA V234A Neutral 9 0.035 SNPs&GO T242K Neutral 5 0.249 PhD-SNP: F[T]=40% F[K]=1% Nali=116 T242K Unclassified NA NA PANTHER: F[T]=NA F[K]=NA T242K Neutral 9 0.064 SNPs&GO Q252R Neutral 7 0.132 PhD-SNP: F[Q]=24% F[R]=18% Nali=141 Q252R Unclassified NA NA PANTHER: F[Q]=NA F[R]=NA Q252R Neutral 9 0.045 SNPs&GO I262L Disease 0 0.517 PhD-SNP: F[I]=34% F[L]=9% Nali=179 I262L Unclassified NA NA PANTHER: F[I]=NA F[L]=NA I262L Neutral 5 0.256 SNPs&GO I272M Neutral 4 0.303 PhD-SNP: F[I]=27% F[M]=1% Nali=181 I272M Unclassified NA NA PANTHER: F[I]=NA F[M]=NA I272M Neutral 7 0.166 SNPs&GO I274N Disease 1 0.535 PhD-SNP: F[I]=11% F[N]=0% Nali=182 I274N Unclassified NA NA PANTHER: F[I]=NA F[N]=NA I274N Neutral 4 0.304 SNPs&GO A286T Neutral 9 0.074 PhD-SNP: F[A]=19% F[T]=7% Nali=184 A286T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A286T Neutral 9 0.035 SNPs&GO E290K Neutral 5 0.253 PhD-SNP: F[E]=31% F[K]=13% Nali=179 E290K Unclassified NA NA PANTHER: F[E]=NA F[K]=NA E290K Neutral 8 0.114 SNPs&GO I292V Neutral 8 0.122 PhD-SNP: F[I]=26% F[V]=12% Nali=173 I292V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I292V Neutral 9 0.062 SNPs&GO R296Q Neutral 8 0.105 PhD-SNP: F[R]=16% F[Q]=22% Nali=179 R296Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R296Q Neutral 9 0.047 SNPs&GO V301A Neutral 4 0.296 PhD-SNP: F[V]=40% F[A]=12% Nali=180 V301A Unclassified NA NA PANTHER: F[V]=NA F[A]=NA V301A Neutral 9 0.075 SNPs&GO I308V Neutral 7 0.160 PhD-SNP: F[I]=19% F[V]=19% Nali=182 I308V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I308V Neutral 9 0.075 SNPs&GO G313A Neutral 8 0.116 PhD-SNP: F[G]=25% F[A]=17% Nali=180 G313A Unclassified NA NA PANTHER: F[G]=NA F[A]=NA G313A Neutral 9 0.035 SNPs&GO T335N Neutral 4 0.300 PhD-SNP: F[T]=16% F[N]=4% Nali=182 T335N Unclassified NA NA PANTHER: F[T]=NA F[N]=NA T335N Neutral 7 0.147 SNPs&GO R339H Neutral 5 0.227 PhD-SNP: F[R]=24% F[H]=5% Nali=175 R339H Unclassified NA NA PANTHER: F[R]=NA F[H]=NA R339H Neutral 8 0.094 SNPs&GO R339S Neutral 6 0.203 PhD-SNP: F[R]=24% F[S]=6% Nali=175 R339S Unclassified NA NA PANTHER: F[R]=NA F[S]=NA R339S Neutral 8 0.091 SNPs&GO N393S Neutral 1 0.446 PhD-SNP: F[N]=37% F[S]=8% Nali=176 N393S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N393S Neutral 6 0.184 SNPs&GO A399T Neutral 6 0.203 PhD-SNP: F[A]=17% F[T]=3% Nali=179 A399T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A399T Neutral 8 0.113 SNPs&GO P415T Disease 2 0.586 PhD-SNP: F[P]=69% F[T]=1% Nali=175 P415T Unclassified NA NA PANTHER: F[P]=NA F[T]=NA P415T Neutral 8 0.116 SNPs&GO H432R Neutral 7 0.144 PhD-SNP: F[H]=14% F[R]=13% Nali=153 H432R Unclassified NA NA PANTHER: F[H]=NA F[R]=NA H432R Neutral 9 0.037 SNPs&GO P476L Disease 1 0.528 PhD-SNP: F[P]=59% F[L]=0% Nali=169 P476L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P476L Neutral 7 0.136 SNPs&GO E477Q Neutral 2 0.376 PhD-SNP: F[E]=43% F[Q]=4% Nali=170 E477Q Unclassified NA NA PANTHER: F[E]=NA F[Q]=NA E477Q Neutral 8 0.106 SNPs&GO M489T Neutral 7 0.161 PhD-SNP: F[M]=8% F[T]=1% Nali=168 M489T Unclassified NA NA PANTHER: F[M]=NA F[T]=NA M489T Neutral 8 0.091 SNPs&GO R512Q Neutral 6 0.177 PhD-SNP: F[R]=30% F[Q]=8% Nali=144 R512Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R512Q Neutral 9 0.067 SNPs&GO L522V Neutral 8 0.121 PhD-SNP: F[L]=32% F[V]=1% Nali=111 L522V Unclassified NA NA PANTHER: F[L]=NA F[V]=NA L522V Neutral 9 0.037 SNPs&GO G530D Neutral 6 0.191 PhD-SNP: F[G]=49% F[D]=6% Nali=34 G530D Unclassified NA NA PANTHER: F[G]=NA F[D]=NA G530D Neutral 9 0.066 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. ** ** ** **********************************************************************************************