K_net: Lysine Malonylation Sites Identification With Neural Network

Jin Sun,Yuehui Chen,Yi Cao,Wenzheng Bao,Dong Wang

doi:10.1109/access.2019.2961941

Jin Sun, Yuehui Chen + Show 3 more

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https://doi.org/10.1109/access.2019.2961941

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Journal: IEEE Access	Publication Date: Jan 1, 2020
Citations: 24	License type: CC BY 4.0

Affiliation: University of Jinan, Xuzhou University of Technology

Abstract

Lysine Malonylation (Kmal) is a newly discovered protein post-translational modifications (PTMs) type, which plays an important role in many biological processes. Therefore, identifying and understanding Kmal sites is very critical in the studies of biology and diseases. The typical methods are time-wasting and expensive. Nowadays, many researchers have proposed machine learning (ML) methods to deal with PTMs’s identification issue. Especially, some deep learning (DL) methods are also utilized in this field. In this work, we proposed K_net, which employed Convolutional Neural Network to identify the potential sites. Meanwhile, we proposed a new verification method Split to Equal Validation (SEV), which can well solve the impact of sample imbalance on prediction results. More Specifically, Acc, Sn, Sp, MCC and AUC values were adopted to evaluate the prediction performance of predictors. In total, CNN_Kmal achieved the better performance than other methods.

Highlights

Protein post-translational modification (PTM) is a key mechanism that influence almost all aspects of cell biology and pathogenesis [1], [2]
EAAC, EBPR and EAACon are different feature extraction shames, EAAC were developed by chen et al based on AAC encoding, EBPR were proposed by Han et al and EAACon were proposed by us based on EAAC and Convolutional Neural Network
We proposed a novel validation strategy, Split to Equal Validation (SEV), for both dataset process and performance evaluation as well as k-fold cross validation

Summary

Introduction

Protein post-translational modification (PTM) is a key mechanism that influence almost all aspects of cell biology and pathogenesis [1], [2]. Lysine glycation is characterized as an important regulator for aging and pathogenesis of diabetes. Acetylation, another important type of lysine PTM, is associated with protein stability, protein–protein interactions and cellular metabolism [6]–[8]. More than 20 type of PTM s have been characterized, such as lysine acetylation, glycation and methylation [15]–[18]. There are many researches related to Kmal in recent researches: For instance, malonylation on K184 of glyceraldehyde 3-phosphate dehydrogenase regulates the activity of this key metabolic enzyme, The associate editor coordinating the review of this manuscript and approving it for publication was Yongtao Hao

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