********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: fileseq.seq Mutation Prediction RI Probability Method S28I Neutral 1 0.446 PhD-SNP: F[S]=12% F[I]=1% Nali=477 S28I Neutral 1 0.455 PANTHER: F[S]=32% F[I]=1% S28I Neutral 2 0.401 SNPs&GO W30C Neutral 1 0.436 PhD-SNP: F[W]=12% F[C]=1% Nali=463 W30C Disease 8 0.875 PANTHER: F[W]=75% F[C]=0% W30C Disease 5 0.732 SNPs&GO L32V Neutral 3 0.364 PhD-SNP: F[L]=47% F[V]=1% Nali=637 L32V Disease 3 0.661 PANTHER: F[L]=78% F[V]=3% L32V Neutral 1 0.459 SNPs&GO I42M Neutral 1 0.440 PhD-SNP: F[I]=40% F[M]=1% Nali=753 I42M Neutral 3 0.346 PANTHER: F[I]=35% F[M]=3% I42M Neutral 6 0.200 SNPs&GO Q62H Disease 0 0.509 PhD-SNP: F[Q]=10% F[H]=1% Nali=888 Q62H Neutral 5 0.227 PANTHER: F[Q]=11% F[H]=2% Q62H Neutral 7 0.138 SNPs&GO T69R Disease 6 0.812 PhD-SNP: F[T]=45% F[R]=3% Nali=898 T69R Disease 7 0.865 PANTHER: F[T]=77% F[R]=0% T69R Disease 7 0.837 SNPs&GO G99S Neutral 1 0.458 PhD-SNP: F[G]=48% F[S]=11% Nali=909 G99S Disease 2 0.575 PANTHER: F[G]=77% F[S]=2% G99S Neutral 1 0.462 SNPs&GO G113E Disease 8 0.891 PhD-SNP: F[G]=80% F[E]=0% Nali=913 G113E Disease 10 0.992 PANTHER: F[G]=97% F[E]=0% G113E Disease 8 0.876 SNPs&GO P120S Neutral 2 0.424 PhD-SNP: F[P]=24% F[S]=2% Nali=917 P120S Neutral 6 0.202 PANTHER: F[P]=45% F[S]=10% P120S Neutral 7 0.166 SNPs&GO R127L Disease 8 0.912 PhD-SNP: F[R]=67% F[L]=0% Nali=942 R127L Disease 2 0.616 PANTHER: F[R]=65% F[L]=1% R127L Disease 6 0.823 SNPs&GO L133I Disease 4 0.702 PhD-SNP: F[L]=83% F[I]=2% Nali=945 L133I Neutral 3 0.336 PANTHER: F[L]=65% F[I]=6% L133I Neutral 2 0.418 SNPs&GO A151T Disease 2 0.606 PhD-SNP: F[A]=53% F[T]=3% Nali=949 A151T Neutral 5 0.261 PANTHER: F[A]=25% F[T]=4% A151T Neutral 6 0.218 SNPs&GO A157T Neutral 4 0.314 PhD-SNP: F[A]=24% F[T]=4% Nali=951 A157T Neutral 5 0.243 PANTHER: F[A]=27% F[T]=4% A157T Neutral 8 0.121 SNPs&GO T161S Neutral 7 0.162 PhD-SNP: F[T]=24% F[S]=9% Nali=959 T161S Neutral 2 0.380 PANTHER: F[T]=58% F[S]=5% T161S Neutral 7 0.153 SNPs&GO P165L Disease 3 0.665 PhD-SNP: F[P]=66% F[L]=4% Nali=934 P165L Disease 4 0.723 PANTHER: F[P]=77% F[L]=1% P165L Disease 2 0.619 SNPs&GO D167G Disease 6 0.804 PhD-SNP: F[D]=66% F[G]=0% Nali=957 D167G Disease 6 0.825 PANTHER: F[D]=83% F[G]=1% D167G Disease 6 0.781 SNPs&GO L171F Neutral 2 0.398 PhD-SNP: F[L]=26% F[F]=4% Nali=962 L171F Neutral 2 0.393 PANTHER: F[L]=41% F[F]=3% L171F Neutral 5 0.229 SNPs&GO A175T Disease 4 0.715 PhD-SNP: F[A]=64% F[T]=7% Nali=962 A175T Neutral 1 0.439 PANTHER: F[A]=62% F[T]=4% A175T Disease 3 0.637 SNPs&GO D182G Disease 1 0.549 PhD-SNP: F[D]=2% F[G]=3% Nali=969 D182G Disease 1 0.562 PANTHER: F[D]=67% F[G]=2% D182G Disease 4 0.680 SNPs&GO D182N Neutral 0 0.475 PhD-SNP: F[D]=2% F[N]=2% Nali=969 D182N Neutral 0 0.494 PANTHER: F[D]=67% F[N]=3% D182N Disease 2 0.581 SNPs&GO I183M Neutral 4 0.283 PhD-SNP: F[I]=41% F[M]=15% Nali=974 I183M Disease 0 0.513 PANTHER: F[I]=54% F[M]=2% I183M Neutral 4 0.288 SNPs&GO L184F Disease 1 0.565 PhD-SNP: F[L]=18% F[F]=0% Nali=973 L184F Neutral 0 0.495 PANTHER: F[L]=65% F[F]=3% L184F Neutral 1 0.462 SNPs&GO F207L Neutral 1 0.430 PhD-SNP: F[F]=30% F[L]=16% Nali=935 F207L Neutral 3 0.350 PANTHER: F[F]=64% F[L]=6% F207L Neutral 2 0.403 SNPs&GO P222S Disease 3 0.631 PhD-SNP: F[P]=74% F[S]=7% Nali=937 P222S Neutral 8 0.102 PANTHER: F[P]=30% F[S]=17% P222S Neutral 7 0.167 SNPs&GO K237Q Neutral 4 0.306 PhD-SNP: F[K]=37% F[Q]=9% Nali=952 K237Q Neutral 4 0.314 PANTHER: F[K]=44% F[Q]=5% K237Q Neutral 6 0.188 SNPs&GO H254Y Neutral 7 0.166 PhD-SNP: F[H]=2% F[Y]=6% Nali=962 H254Y Neutral 6 0.215 PANTHER: F[H]=7% F[Y]=1% H254Y Neutral 9 0.048 SNPs&GO L257V Neutral 4 0.312 PhD-SNP: F[L]=44% F[V]=1% Nali=959 L257V Neutral 3 0.369 PANTHER: F[L]=65% F[V]=5% L257V Neutral 6 0.208 SNPs&GO C261S Neutral 8 0.116 PhD-SNP: F[C]=6% F[S]=15% Nali=954 C261S Disease 1 0.554 PANTHER: F[C]=73% F[S]=2% C261S Neutral 3 0.363 SNPs&GO P262S Neutral 1 0.440 PhD-SNP: F[P]=56% F[S]=2% Nali=954 P262S Neutral 7 0.138 PANTHER: F[P]=35% F[S]=13% P262S Neutral 8 0.094 SNPs&GO R263Q Disease 2 0.600 PhD-SNP: F[R]=79% F[Q]=8% Nali=960 R263Q Disease 1 0.529 PANTHER: F[R]=65% F[Q]=2% R263Q Disease 1 0.530 SNPs&GO D267E Disease 3 0.651 PhD-SNP: F[D]=88% F[E]=5% Nali=972 D267E Disease 5 0.744 PANTHER: F[D]=85% F[E]=2% D267E Disease 4 0.698 SNPs&GO D287E Neutral 7 0.158 PhD-SNP: F[D]=20% F[E]=43% Nali=964 D287E Neutral 8 0.110 PANTHER: F[D]=40% F[E]=20% D287E Neutral 8 0.118 SNPs&GO V291M Neutral 7 0.157 PhD-SNP: F[V]=8% F[M]=14% Nali=968 V291M Neutral 0 0.493 PANTHER: F[V]=41% F[M]=2% V291M Neutral 6 0.216 SNPs&GO G311E Disease 5 0.760 PhD-SNP: F[G]=33% F[E]=0% Nali=983 G311E Disease 4 0.694 PANTHER: F[G]=77% F[E]=1% G311E Disease 5 0.765 SNPs&GO E320A Disease 1 0.550 PhD-SNP: F[E]=42% F[A]=1% Nali=981 E320A Disease 0 0.511 PANTHER: F[E]=62% F[A]=2% E320A Neutral 1 0.432 SNPs&GO P339S Disease 6 0.792 PhD-SNP: F[P]=88% F[S]=0% Nali=967 P339S Disease 2 0.605 PANTHER: F[P]=77% F[S]=2% P339S Disease 3 0.626 SNPs&GO P339T Disease 5 0.766 PhD-SNP: F[P]=88% F[T]=0% Nali=967 P339T Disease 3 0.667 PANTHER: F[P]=77% F[T]=1% P339T Disease 2 0.608 SNPs&GO I341M Neutral 8 0.097 PhD-SNP: F[I]=9% F[M]=28% Nali=982 I341M Neutral 1 0.445 PANTHER: F[I]=41% F[M]=2% I341M Neutral 6 0.186 SNPs&GO D351G Disease 5 0.726 PhD-SNP: F[D]=28% F[G]=0% Nali=983 D351G Disease 1 0.562 PANTHER: F[D]=67% F[G]=2% D351G Disease 3 0.667 SNPs&GO F360L Neutral 3 0.365 PhD-SNP: F[F]=32% F[L]=9% Nali=980 F360L Neutral 3 0.350 PANTHER: F[F]=64% F[L]=6% F360L Neutral 2 0.386 SNPs&GO L368P Disease 6 0.818 PhD-SNP: F[L]=35% F[P]=1% Nali=978 L368P Disease 6 0.800 PANTHER: F[L]=65% F[P]=0% L368P Disease 6 0.821 SNPs&GO R374L Disease 5 0.739 PhD-SNP: F[R]=25% F[L]=0% Nali=981 R374L Neutral 3 0.367 PANTHER: F[R]=28% F[L]=2% R374L Disease 0 0.511 SNPs&GO P384T Disease 7 0.845 PhD-SNP: F[P]=90% F[T]=0% Nali=980 P384T Disease 3 0.667 PANTHER: F[P]=77% F[T]=1% P384T Disease 3 0.658 SNPs&GO D399H Disease 7 0.829 PhD-SNP: F[D]=91% F[H]=0% Nali=970 D399H Disease 5 0.727 PANTHER: F[D]=67% F[H]=1% D399H Disease 4 0.709 SNPs&GO E402D Neutral 4 0.306 PhD-SNP: F[E]=25% F[D]=0% Nali=969 E402D Neutral 3 0.362 PANTHER: F[E]=62% F[D]=5% E402D Neutral 4 0.299 SNPs&GO V464I Neutral 7 0.171 PhD-SNP: F[V]=33% F[I]=3% Nali=645 V464I Unclassified NA NA PANTHER: F[V]=NA F[I]=NA V464I Neutral 9 0.041 SNPs&GO C480F Neutral 0 0.482 PhD-SNP: F[C]=4% F[F]=1% Nali=677 C480F Unclassified NA NA PANTHER: F[C]=NA F[F]=NA C480F Neutral 6 0.190 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. ** ** ** **********************************************************************************************