********************************************************************************************** ** ** ** 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 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 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 V79A Disease 5 0.747 PhD-SNP: F[V]=74% F[A]=0% Nali=911 V79A Neutral 1 0.429 PANTHER: F[V]=57% F[A]=3% V79A Disease 1 0.532 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 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 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 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 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 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 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 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 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 V388L Neutral 6 0.203 PhD-SNP: F[V]=12% F[L]=5% Nali=971 V388L Neutral 4 0.299 PANTHER: F[V]=57% F[L]=7% V388L Neutral 5 0.253 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 D468Y Disease 4 0.691 PhD-SNP: F[D]=35% F[Y]=0% Nali=732 D468Y Unclassified NA NA PANTHER: F[D]=NA F[Y]=NA D468Y Neutral 5 0.228 SNPs&GO F478V Disease 3 0.633 PhD-SNP: F[F]=38% F[V]=9% Nali=675 F478V Unclassified NA NA PANTHER: F[F]=NA F[V]=NA F478V Neutral 5 0.254 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. ** ** ** **********************************************************************************************