********************************************************************************************** ** ** ** SNPs&GO ** ** Predicting disease associated variation using GO terms ** ** ** ********************************************************************************************** Sequence File: CAC1C_HUMAN.seq Mutation Prediction RI Probability Method N3S Neutral 2 0.388 PhD-SNP: F[N]=100% F[S]=0% Nali=15 N3S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N3S Disease 7 0.873 SNPs&GO E4D Neutral 4 0.293 PhD-SNP: F[E]=100% F[D]=0% Nali=16 E4D Unclassified NA NA PANTHER: F[E]=NA F[D]=NA E4D Disease 6 0.809 SNPs&GO N5H Neutral 1 0.438 PhD-SNP: F[N]=76% F[H]=0% Nali=16 N5H Unclassified NA NA PANTHER: F[N]=NA F[H]=NA N5H Disease 5 0.763 SNPs&GO N5K Disease 1 0.553 PhD-SNP: F[N]=76% F[K]=0% Nali=16 N5K Unclassified NA NA PANTHER: F[N]=NA F[K]=NA N5K Disease 8 0.889 SNPs&GO N5S Neutral 6 0.178 PhD-SNP: F[N]=76% F[S]=18% Nali=16 N5S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N5S Disease 1 0.572 SNPs&GO R7K Neutral 3 0.356 PhD-SNP: F[R]=78% F[K]=6% Nali=17 R7K Unclassified NA NA PANTHER: F[R]=NA F[K]=NA R7K Disease 5 0.765 SNPs&GO R7S Disease 2 0.609 PhD-SNP: F[R]=78% F[S]=0% Nali=17 R7S Unclassified NA NA PANTHER: F[R]=NA F[S]=NA R7S Disease 7 0.859 SNPs&GO R7T Disease 4 0.703 PhD-SNP: F[R]=78% F[T]=0% Nali=17 R7T Unclassified NA NA PANTHER: F[R]=NA F[T]=NA R7T Disease 8 0.876 SNPs&GO M8R Disease 5 0.767 PhD-SNP: F[M]=83% F[R]=0% Nali=17 M8R Unclassified NA NA PANTHER: F[M]=NA F[R]=NA M8R Disease 9 0.947 SNPs&GO P11A Disease 1 0.553 PhD-SNP: F[P]=86% F[A]=0% Nali=20 P11A Unclassified NA NA PANTHER: F[P]=NA F[A]=NA P11A Disease 6 0.793 SNPs&GO E12G Disease 1 0.538 PhD-SNP: F[E]=77% F[G]=0% Nali=21 E12G Unclassified NA NA PANTHER: F[E]=NA F[G]=NA E12G Disease 7 0.833 SNPs&GO E12V Disease 4 0.706 PhD-SNP: F[E]=77% F[V]=0% Nali=21 E12V Unclassified NA NA PANTHER: F[E]=NA F[V]=NA E12V Disease 8 0.881 SNPs&GO E13K Disease 4 0.716 PhD-SNP: F[E]=73% F[K]=0% Nali=21 E13K Unclassified NA NA PANTHER: F[E]=NA F[K]=NA E13K Disease 8 0.901 SNPs&GO S18F Disease 1 0.564 PhD-SNP: F[S]=63% F[F]=3% Nali=29 S18F Unclassified NA NA PANTHER: F[S]=NA F[F]=NA S18F Disease 5 0.740 SNPs&GO N19K Neutral 3 0.357 PhD-SNP: F[N]=70% F[K]=7% Nali=29 N19K Unclassified NA NA PANTHER: F[N]=NA F[K]=NA N19K Disease 4 0.713 SNPs&GO Y20C Disease 1 0.568 PhD-SNP: F[Y]=59% F[C]=0% Nali=33 Y20C Unclassified NA NA PANTHER: F[Y]=NA F[C]=NA Y20C Disease 5 0.736 SNPs&GO Y20H Neutral 7 0.156 PhD-SNP: F[Y]=59% F[H]=18% Nali=33 Y20H Unclassified NA NA PANTHER: F[Y]=NA F[H]=NA Y20H Neutral 3 0.327 SNPs&GO G21A Neutral 5 0.233 PhD-SNP: F[G]=57% F[A]=14% Nali=34 G21A Unclassified NA NA PANTHER: F[G]=NA F[A]=NA G21A Neutral 4 0.320 SNPs&GO G21E Disease 3 0.674 PhD-SNP: F[G]=57% F[E]=0% Nali=34 G21E Unclassified NA NA PANTHER: F[G]=NA F[E]=NA G21E Disease 6 0.787 SNPs&GO G21W Disease 4 0.676 PhD-SNP: F[G]=57% F[W]=0% Nali=34 G21W Unclassified NA NA PANTHER: F[G]=NA F[W]=NA G21W Disease 5 0.763 SNPs&GO S22I Disease 4 0.710 PhD-SNP: F[S]=64% F[I]=0% Nali=35 S22I Unclassified NA NA PANTHER: F[S]=NA F[I]=NA S22I Disease 6 0.818 SNPs&GO S22N Neutral 1 0.452 PhD-SNP: F[S]=64% F[N]=3% Nali=35 S22N Unclassified NA NA PANTHER: F[S]=NA F[N]=NA S22N Disease 3 0.628 SNPs&GO P23Q Disease 4 0.692 PhD-SNP: F[P]=80% F[Q]=3% Nali=39 P23Q Unclassified NA NA PANTHER: F[P]=NA F[Q]=NA P23Q Disease 6 0.820 SNPs&GO P23S Disease 2 0.604 PhD-SNP: F[P]=80% F[S]=3% Nali=39 P23S Unclassified NA NA PANTHER: F[P]=NA F[S]=NA P23S Disease 6 0.803 SNPs&GO R24C Disease 3 0.650 PhD-SNP: F[R]=51% F[C]=7% Nali=40 R24C Unclassified NA NA PANTHER: F[R]=NA F[C]=NA R24C Disease 5 0.738 SNPs&GO R24H Disease 1 0.541 PhD-SNP: F[R]=51% F[H]=0% Nali=40 R24H Unclassified NA NA PANTHER: F[R]=NA F[H]=NA R24H Disease 2 0.607 SNPs&GO A26T Disease 3 0.673 PhD-SNP: F[A]=51% F[T]=0% Nali=40 A26T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A26T Disease 6 0.789 SNPs&GO A26V Disease 1 0.552 PhD-SNP: F[A]=51% F[V]=2% Nali=40 A26V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A26V Disease 4 0.690 SNPs&GO H27Q Disease 3 0.662 PhD-SNP: F[H]=69% F[Q]=4% Nali=53 H27Q Unclassified NA NA PANTHER: F[H]=NA F[Q]=NA H27Q Disease 6 0.798 SNPs&GO H27R Disease 5 0.738 PhD-SNP: F[H]=69% F[R]=0% Nali=53 H27R Unclassified NA NA PANTHER: F[H]=NA F[R]=NA H27R Disease 8 0.888 SNPs&GO A28T Disease 5 0.732 PhD-SNP: F[A]=63% F[T]=2% Nali=53 A28T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A28T Disease 7 0.860 SNPs&GO M30T Disease 3 0.659 PhD-SNP: F[M]=44% F[T]=2% Nali=42 M30T Unclassified NA NA PANTHER: F[M]=NA F[T]=NA M30T Disease 6 0.815 SNPs&GO M30V Disease 1 0.552 PhD-SNP: F[M]=44% F[V]=0% Nali=42 M30V Unclassified NA NA PANTHER: F[M]=NA F[V]=NA M30V Disease 4 0.693 SNPs&GO N31D Neutral 2 0.414 PhD-SNP: F[N]=40% F[D]=5% Nali=54 N31D Unclassified NA NA PANTHER: F[N]=NA F[D]=NA N31D Disease 4 0.682 SNPs&GO N31S Neutral 2 0.396 PhD-SNP: F[N]=40% F[S]=4% Nali=54 N31S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N31S Disease 2 0.592 SNPs&GO A32T Disease 5 0.736 PhD-SNP: F[A]=67% F[T]=0% Nali=54 A32T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A32T Disease 8 0.882 SNPs&GO N33D Neutral 0 0.478 PhD-SNP: F[N]=59% F[D]=7% Nali=53 N33D Unclassified NA NA PANTHER: F[N]=NA F[D]=NA N33D Disease 5 0.747 SNPs&GO N33S Neutral 1 0.461 PhD-SNP: F[N]=59% F[S]=7% Nali=53 N33S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N33S Disease 4 0.677 SNPs&GO A34E Disease 5 0.729 PhD-SNP: F[A]=29% F[E]=3% Nali=64 A34E Unclassified NA NA PANTHER: F[A]=NA F[E]=NA A34E Disease 8 0.881 SNPs&GO A34V Disease 1 0.561 PhD-SNP: F[A]=29% F[V]=2% Nali=64 A34V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A34V Disease 4 0.723 SNPs&GO A35E Disease 7 0.841 PhD-SNP: F[A]=60% F[E]=1% Nali=69 A35E Unclassified NA NA PANTHER: F[A]=NA F[E]=NA A35E Disease 9 0.941 SNPs&GO A36V Disease 1 0.541 PhD-SNP: F[A]=30% F[V]=0% Nali=69 A36V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A36V Disease 4 0.698 SNPs&GO G37E Disease 5 0.774 PhD-SNP: F[G]=69% F[E]=1% Nali=70 G37E Unclassified NA NA PANTHER: F[G]=NA F[E]=NA G37E Disease 8 0.888 SNPs&GO G37R Disease 6 0.813 PhD-SNP: F[G]=69% F[R]=0% Nali=70 G37R Unclassified NA NA PANTHER: F[G]=NA F[R]=NA G37R Disease 8 0.922 SNPs&GO A39V Disease 2 0.588 PhD-SNP: F[A]=35% F[V]=0% Nali=76 A39V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A39V Disease 5 0.755 SNPs&GO E41K Disease 4 0.683 PhD-SNP: F[E]=55% F[K]=3% Nali=77 E41K Unclassified NA NA PANTHER: F[E]=NA F[K]=NA E41K Disease 6 0.804 SNPs&GO E41V Disease 2 0.597 PhD-SNP: F[E]=55% F[V]=4% Nali=77 E41V Unclassified NA NA PANTHER: F[E]=NA F[V]=NA E41V Disease 5 0.731 SNPs&GO H42R Disease 3 0.633 PhD-SNP: F[H]=44% F[R]=0% Nali=77 H42R Unclassified NA NA PANTHER: F[H]=NA F[R]=NA H42R Disease 7 0.834 SNPs&GO P44A Neutral 4 0.320 PhD-SNP: F[P]=84% F[A]=0% Nali=90 P44A Unclassified NA NA PANTHER: F[P]=NA F[A]=NA P44A Disease 2 0.607 SNPs&GO P44S Neutral 2 0.407 PhD-SNP: F[P]=84% F[S]=5% Nali=90 P44S Unclassified NA NA PANTHER: F[P]=NA F[S]=NA P44S Disease 4 0.721 SNPs&GO T45I Neutral 2 0.376 PhD-SNP: F[T]=38% F[I]=2% Nali=91 T45I Unclassified NA NA PANTHER: F[T]=NA F[I]=NA T45I Disease 3 0.628 SNPs&GO T45N Neutral 5 0.250 PhD-SNP: F[T]=38% F[N]=12% Nali=91 T45N Unclassified NA NA PANTHER: F[T]=NA F[N]=NA T45N Neutral 0 0.488 SNPs&GO T45P Disease 1 0.561 PhD-SNP: F[T]=38% F[P]=1% Nali=91 T45P Unclassified NA NA PANTHER: F[T]=NA F[P]=NA T45P Disease 3 0.673 SNPs&GO T45S Neutral 7 0.151 PhD-SNP: F[T]=38% F[S]=7% Nali=91 T45S Unclassified NA NA PANTHER: F[T]=NA F[S]=NA T45S Neutral 3 0.326 SNPs&GO P46L Neutral 1 0.429 PhD-SNP: F[P]=49% F[L]=0% Nali=92 P46L Unclassified NA NA PANTHER: F[P]=NA F[L]=NA P46L Disease 4 0.711 SNPs&GO P46S Neutral 7 0.155 PhD-SNP: F[P]=49% F[S]=16% Nali=92 P46S Unclassified NA NA PANTHER: F[P]=NA F[S]=NA P46S Neutral 2 0.385 SNPs&GO A48D Disease 3 0.645 PhD-SNP: F[A]=33% F[D]=0% Nali=95 A48D Unclassified NA NA PANTHER: F[A]=NA F[D]=NA A48D Disease 7 0.839 SNPs&GO A48P Neutral 0 0.480 PhD-SNP: F[A]=33% F[P]=9% Nali=95 A48P Unclassified NA NA PANTHER: F[A]=NA F[P]=NA A48P Disease 4 0.694 SNPs&GO A48S Neutral 5 0.274 PhD-SNP: F[A]=33% F[S]=4% Nali=95 A48S Unclassified NA NA PANTHER: F[A]=NA F[S]=NA A48S Disease 2 0.581 SNPs&GO S51L Disease 2 0.609 PhD-SNP: F[S]=64% F[L]=1% Nali=101 S51L Unclassified NA NA PANTHER: F[S]=NA F[L]=NA S51L Disease 6 0.809 SNPs&GO W52R Disease 4 0.722 PhD-SNP: F[W]=56% F[R]=1% Nali=101 W52R Unclassified NA NA PANTHER: F[W]=NA F[R]=NA W52R Disease 8 0.900 SNPs&GO Q53E Neutral 7 0.135 PhD-SNP: F[Q]=46% F[E]=16% Nali=103 Q53E Unclassified NA NA PANTHER: F[Q]=NA F[E]=NA Q53E Disease 1 0.546 SNPs&GO A54G Neutral 1 0.469 PhD-SNP: F[A]=52% F[G]=2% Nali=110 A54G Unclassified NA NA PANTHER: F[A]=NA F[G]=NA A54G Disease 7 0.828 SNPs&GO A54V Neutral 3 0.363 PhD-SNP: F[A]=52% F[V]=6% Nali=110 A54V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A54V Disease 5 0.740 SNPs&GO A55D Disease 6 0.797 PhD-SNP: F[A]=56% F[D]=1% Nali=112 A55D Unclassified NA NA PANTHER: F[A]=NA F[D]=NA A55D Disease 9 0.946 SNPs&GO A55T Neutral 1 0.442 PhD-SNP: F[A]=56% F[T]=3% Nali=112 A55T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A55T Disease 6 0.775 SNPs&GO I56M Neutral 2 0.389 PhD-SNP: F[I]=55% F[M]=1% Nali=111 I56M Unclassified NA NA PANTHER: F[I]=NA F[M]=NA I56M Disease 4 0.706 SNPs&GO D57N Neutral 1 0.454 PhD-SNP: F[D]=62% F[N]=11% Nali=108 D57N Unclassified NA NA PANTHER: F[D]=NA F[N]=NA D57N Disease 5 0.773 SNPs&GO A59S Neutral 0 0.484 PhD-SNP: F[A]=54% F[S]=5% Nali=123 A59S Unclassified NA NA PANTHER: F[A]=NA F[S]=NA A59S Disease 6 0.825 SNPs&GO A59V Disease 1 0.556 PhD-SNP: F[A]=54% F[V]=2% Nali=123 A59V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A59V Disease 7 0.843 SNPs&GO R60P Disease 6 0.790 PhD-SNP: F[R]=56% F[P]=3% Nali=127 R60P Unclassified NA NA PANTHER: F[R]=NA F[P]=NA R60P Disease 8 0.907 SNPs&GO R60Q Neutral 1 0.438 PhD-SNP: F[R]=56% F[Q]=7% Nali=127 R60Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R60Q Disease 4 0.686 SNPs&GO Q61P Disease 7 0.841 PhD-SNP: F[Q]=65% F[P]=2% Nali=126 Q61P Unclassified NA NA PANTHER: F[Q]=NA F[P]=NA Q61P Disease 9 0.945 SNPs&GO K63E Neutral 0 0.494 PhD-SNP: F[K]=40% F[E]=9% Nali=125 K63E Unclassified NA NA PANTHER: F[K]=NA F[E]=NA K63E Disease 6 0.822 SNPs&GO G66V Disease 4 0.677 PhD-SNP: F[G]=62% F[V]=1% Nali=154 G66V Unclassified NA NA PANTHER: F[G]=NA F[V]=NA G66V Disease 7 0.835 SNPs&GO S67N Neutral 2 0.407 PhD-SNP: F[S]=28% F[N]=6% Nali=159 S67N Unclassified NA NA PANTHER: F[S]=NA F[N]=NA S67N Disease 2 0.618 SNPs&GO A68T Neutral 6 0.216 PhD-SNP: F[A]=23% F[T]=8% Nali=163 A68T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A68T Neutral 2 0.401 SNPs&GO A68V Neutral 4 0.305 PhD-SNP: F[A]=23% F[V]=5% Nali=163 A68V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A68V Disease 0 0.503 SNPs&GO N70D Neutral 7 0.169 PhD-SNP: F[N]=26% F[D]=16% Nali=185 N70D Unclassified NA NA PANTHER: F[N]=NA F[D]=NA N70D Neutral 1 0.428 SNPs&GO N70S Neutral 6 0.183 PhD-SNP: F[N]=26% F[S]=10% Nali=185 N70S Unclassified NA NA PANTHER: F[N]=NA F[S]=NA N70S Neutral 3 0.338 SNPs&GO A71T Neutral 5 0.262 PhD-SNP: F[A]=34% F[T]=9% Nali=190 A71T Unclassified NA NA PANTHER: F[A]=NA F[T]=NA A71T Neutral 2 0.386 SNPs&GO A71V Neutral 4 0.321 PhD-SNP: F[A]=34% F[V]=7% Nali=190 A71V Unclassified NA NA PANTHER: F[A]=NA F[V]=NA A71V Neutral 1 0.464 SNPs&GO I73V Neutral 9 0.070 PhD-SNP: F[I]=28% F[V]=14% Nali=202 I73V Unclassified NA NA PANTHER: F[I]=NA F[V]=NA I73V Neutral 7 0.161 SNPs&GO S77G Neutral 8 0.108 PhD-SNP: F[S]=30% F[G]=12% Nali=237 S77G Unclassified NA NA PANTHER: F[S]=NA F[G]=NA S77G Neutral 3 0.345 SNPs&GO S77I Neutral 3 0.359 PhD-SNP: F[S]=30% F[I]=0% Nali=237 S77I Unclassified NA NA PANTHER: F[S]=NA F[I]=NA S77I Disease 2 0.575 SNPs&GO S78T Neutral 6 0.222 PhD-SNP: F[S]=42% F[T]=2% Nali=247 S78T Unclassified NA NA PANTHER: F[S]=NA F[T]=NA S78T Neutral 3 0.335 SNPs&GO T79M Neutral 2 0.390 PhD-SNP: F[T]=51% F[M]=0% Nali=405 T79M Unclassified NA NA PANTHER: F[T]=NA F[M]=NA T79M Disease 4 0.687 SNPs&GO R81Q Neutral 3 0.367 PhD-SNP: F[R]=32% F[Q]=3% Nali=431 R81Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R81Q Disease 1 0.528 SNPs&GO R81W Disease 2 0.616 PhD-SNP: F[R]=32% F[W]=0% Nali=431 R81W Unclassified NA NA PANTHER: F[R]=NA F[W]=NA R81W Disease 5 0.749 SNPs&GO R83Q Neutral 2 0.380 PhD-SNP: F[R]=38% F[Q]=4% Nali=442 R83Q Unclassified NA NA PANTHER: F[R]=NA F[Q]=NA R83Q Disease 2 0.592 SNPs&GO R83W Disease 2 0.600 PhD-SNP: F[R]=38% F[W]=0% Nali=442 R83W Unclassified NA NA PANTHER: F[R]=NA F[W]=NA R83W Disease 6 0.790 SNPs&GO Q84R Neutral 6 0.223 PhD-SNP: F[Q]=27% F[R]=5% Nali=441 Q84R Unclassified NA NA PANTHER: F[Q]=NA F[R]=NA Q84R Disease 1 0.547 SNPs&GO Q85E Neutral 7 0.162 PhD-SNP: F[Q]=23% F[E]=4% Nali=441 Q85E Unclassified NA NA PANTHER: F[Q]=NA F[E]=NA Q85E Neutral 1 0.446 SNPs&GO Q85P Disease 1 0.540 PhD-SNP: F[Q]=23% F[P]=1% Nali=441 Q85P Unclassified NA NA PANTHER: F[Q]=NA F[P]=NA Q85P Disease 4 0.711 SNPs&GO Y86C Neutral 0 0.476 PhD-SNP: F[Y]=55% F[C]=0% Nali=440 Y86C Unclassified NA NA PANTHER: F[Y]=NA F[C]=NA Y86C Disease 5 0.725 SNPs&GO K88E Neutral 3 0.361 PhD-SNP: F[K]=31% F[E]=2% Nali=456 K88E Unclassified NA NA PANTHER: F[K]=NA F[E]=NA K88E Disease 3 0.633 SNPs&GO P89H Neutral 7 0.157 PhD-SNP: F[P]=31% F[H]=2% Nali=493 P89H Unclassified NA NA PANTHER: F[P]=NA F[H]=NA P89H Neutral 2 0.412 SNPs&GO K90Q Neutral 4 0.307 PhD-SNP: F[K]=58% F[Q]=7% Nali=516 K90Q Unclassified NA NA PANTHER: F[K]=NA F[Q]=NA K90Q Disease 0 0.523 SNPs&GO Q92P Disease 0 0.507 PhD-SNP: F[Q]=32% F[P]=2% Nali=534 Q92P Unclassified NA NA PANTHER: F[Q]=NA F[P]=NA Q92P Disease 4 0.690 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. ** ** ** **********************************************************************************************