Comput Biol Chem - Predicting deleterious non-synonymous single nucleotide polymorphisms in signal peptides based on hybrid sequence attributes.

Tópicos

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Resumo

Signal peptides play a crucial role in various biological processes, such as localization of cell surface receptors, translocation of secreted proteins and cell-cell communication. However, the amino acid mutation in signal peptides, also called non-synonymous single nucleotide polymorphisms (nsSNPs or SAPs) may lead to the loss of their functions. In the present study, a computational method was proposed for predicting deleterious nsSNPs in signal peptides based on random forest (RF) by incorporating position specific scoring matrix (PSSM) profile, SignalP score and physicochemical properties. These features were optimized by the maximum relevance minimum redundancy (mRMR) method. Then, a cost matrix was used to minimize the effect of the imbalanced data classification problem that usually occurred in nsSNPs prediction. The method achieved an overall accuracy of 84.5% and the area under the ROC curve (AUC) of 0.822 by Jackknife test, when the optimal subset included 10 features. Furthermore, on the same dataset, we compared our predictor with other existing methods, including R-score-based method and D-score-based methods, and the result of our method was superior to those of the two methods. The satisfactory performance suggests that our method is effective in predicting the deleterious nsSNPs in signal peptides.

Resumo Limpo

signal peptid play crucial role various biolog process local cell surfac receptor transloc secret protein cellcel communic howev amino acid mutat signal peptid also call nonsynonym singl nucleotid polymorph nssnps sap may lead loss function present studi comput method propos predict deleteri nssnps signal peptid base random forest rf incorpor posit specif score matrix pssm profil signalp score physicochem properti featur optim maximum relev minimum redund mrmr method cost matrix use minim effect imbalanc data classif problem usual occur nssnps predict method achiev overal accuraci area roc curv auc jackknif test optim subset includ featur furthermor dataset compar predictor exist method includ rscorebas method dscorebas method result method superior two method satisfactori perform suggest method effect predict deleteri nssnps signal peptid

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