piEnPred: a bi-layered discriminative model for enhancers and their subtypes via novel cascade multi-level subset feature selection algorithm

Abstract

Enhancers are short DNA cis-elements that can be bound by proteins (activators) to increase the possibility that transcription of a particular gene will occur. The Enhancers perform a significant role in the formation of proteins and regulating the gene transcription process. Human diseases such as cancer, inflammatory bowel disease, Parkinson’s, addiction, and schizophrenia are due to genetic variation in enhancers. In the current study, we havemade an effort by building, amore robust and novel computational a bi-layered model. The representative feature vector was constructed over a linear combination of six features. The optimum Hybrid feature vector was obtained via the Novel Cascade Multi-Level Subset Feature selection (CMSFS) algorithm. The first layer predicts the enhancer, and the secondary layer carries the prediction of their subtypes. The baseline model obtained 87.88% of accuracy, 95.29% of sensitivity, 80.47% of specificity, 0.766 of MCC, and 0.9603 of a roc value on Layer-1. Similarly, the model obtained 68.24%, 65.54%, 70.95%, 0.3654, and 0.7568 as an Accuracy, sensitivity, specificity, MCC, and ROC values on layer-2 respectively. Over an independent dataset on layer-1, the piEnPred secured 80.4% accuracy, 82.5% of sensitivity, 78.4% of specificity, and 0.6099 as MCC, respectively. Subsequently, the proposed predictor obtained 72.5% of accuracy, 70.0% of sensitivity, 75% of specificity, and 0.4506 of MCC on layer-2, respectively. The proposed method remarkably performed in contrast to other state-of-the-art predictors. For the convenience of most experimental scientists, a user-friendly and publicly freely accessible web server@/bienhancer dot pythonanywhere dot com has been developed.

Keywords

enhancer / enhancer types / novel CM-SFS algorithm / feature selection / SVM

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