A deep learning method to more accurately recall known lysine acetylation sites
Abstract Background Lysine acetylation in protein is one of the most important post-translational modifications (PTMs). It plays an important role in essential biological processes and is related to various diseases. To obtain a comprehensive understanding of regulatory mechanism of lysine acetylati...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2019-01-01
|
Series: | BMC Bioinformatics |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s12859-019-2632-9 |
id |
doaj-9dd8b78065654fda831c5370138e9625 |
---|---|
record_format |
Article |
spelling |
doaj-9dd8b78065654fda831c5370138e96252020-11-25T01:12:52ZengBMCBMC Bioinformatics1471-21052019-01-0120111110.1186/s12859-019-2632-9A deep learning method to more accurately recall known lysine acetylation sitesMeiqi Wu0Yingxi Yang1Hui Wang2Yan Xu3Department of Information and Computer Science, University of Science and Technology BeijingDepartment of Information and Computer Science, University of Science and Technology BeijingInstitute of Computing Technology, Chinese Academy of SciencesDepartment of Information and Computer Science, University of Science and Technology BeijingAbstract Background Lysine acetylation in protein is one of the most important post-translational modifications (PTMs). It plays an important role in essential biological processes and is related to various diseases. To obtain a comprehensive understanding of regulatory mechanism of lysine acetylation, the key is to identify lysine acetylation sites. Previously, several shallow machine learning algorithms had been applied to predict lysine modification sites in proteins. However, shallow machine learning has some disadvantages. For instance, it is not as effective as deep learning for processing big data. Results In this work, a novel predictor named DeepAcet was developed to predict acetylation sites. Six encoding schemes were adopted, including a one-hot, BLOSUM62 matrix, a composition of K-space amino acid pairs, information gain, physicochemical properties, and a position specific scoring matrix to represent the modified residues. A multilayer perceptron (MLP) was utilized to construct a model to predict lysine acetylation sites in proteins with many different features. We also integrated all features and implemented the feature selection method to select a feature set that contained 2199 features. As a result, the best prediction achieved 84.95% accuracy, 83.45% specificity, 86.44% sensitivity, 0.8540 AUC, and 0.6993 MCC in a 10-fold cross-validation. For an independent test set, the prediction achieved 84.87% accuracy, 83.46% specificity, 86.28% sensitivity, 0.8407 AUC, and 0.6977 MCC. Conclusion The predictive performance of our DeepAcet is better than that of other existing methods. DeepAcet can be freely downloaded from https://github.com/Sunmile/DeepAcet.http://link.springer.com/article/10.1186/s12859-019-2632-9Lysine acetylationPTMsDeep learning |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Meiqi Wu Yingxi Yang Hui Wang Yan Xu |
spellingShingle |
Meiqi Wu Yingxi Yang Hui Wang Yan Xu A deep learning method to more accurately recall known lysine acetylation sites BMC Bioinformatics Lysine acetylation PTMs Deep learning |
author_facet |
Meiqi Wu Yingxi Yang Hui Wang Yan Xu |
author_sort |
Meiqi Wu |
title |
A deep learning method to more accurately recall known lysine acetylation sites |
title_short |
A deep learning method to more accurately recall known lysine acetylation sites |
title_full |
A deep learning method to more accurately recall known lysine acetylation sites |
title_fullStr |
A deep learning method to more accurately recall known lysine acetylation sites |
title_full_unstemmed |
A deep learning method to more accurately recall known lysine acetylation sites |
title_sort |
deep learning method to more accurately recall known lysine acetylation sites |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2019-01-01 |
description |
Abstract Background Lysine acetylation in protein is one of the most important post-translational modifications (PTMs). It plays an important role in essential biological processes and is related to various diseases. To obtain a comprehensive understanding of regulatory mechanism of lysine acetylation, the key is to identify lysine acetylation sites. Previously, several shallow machine learning algorithms had been applied to predict lysine modification sites in proteins. However, shallow machine learning has some disadvantages. For instance, it is not as effective as deep learning for processing big data. Results In this work, a novel predictor named DeepAcet was developed to predict acetylation sites. Six encoding schemes were adopted, including a one-hot, BLOSUM62 matrix, a composition of K-space amino acid pairs, information gain, physicochemical properties, and a position specific scoring matrix to represent the modified residues. A multilayer perceptron (MLP) was utilized to construct a model to predict lysine acetylation sites in proteins with many different features. We also integrated all features and implemented the feature selection method to select a feature set that contained 2199 features. As a result, the best prediction achieved 84.95% accuracy, 83.45% specificity, 86.44% sensitivity, 0.8540 AUC, and 0.6993 MCC in a 10-fold cross-validation. For an independent test set, the prediction achieved 84.87% accuracy, 83.46% specificity, 86.28% sensitivity, 0.8407 AUC, and 0.6977 MCC. Conclusion The predictive performance of our DeepAcet is better than that of other existing methods. DeepAcet can be freely downloaded from https://github.com/Sunmile/DeepAcet. |
topic |
Lysine acetylation PTMs Deep learning |
url |
http://link.springer.com/article/10.1186/s12859-019-2632-9 |
work_keys_str_mv |
AT meiqiwu adeeplearningmethodtomoreaccuratelyrecallknownlysineacetylationsites AT yingxiyang adeeplearningmethodtomoreaccuratelyrecallknownlysineacetylationsites AT huiwang adeeplearningmethodtomoreaccuratelyrecallknownlysineacetylationsites AT yanxu adeeplearningmethodtomoreaccuratelyrecallknownlysineacetylationsites AT meiqiwu deeplearningmethodtomoreaccuratelyrecallknownlysineacetylationsites AT yingxiyang deeplearningmethodtomoreaccuratelyrecallknownlysineacetylationsites AT huiwang deeplearningmethodtomoreaccuratelyrecallknownlysineacetylationsites AT yanxu deeplearningmethodtomoreaccuratelyrecallknownlysineacetylationsites |
_version_ |
1725164654788870144 |