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DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites

BACKGROUND: Addressing the laborious nature of traditional biological experiments by using an efficient computational approach to analyze RNA-binding proteins (RBPs) binding sites has always been a challenging task. RBPs play a vital role in post-transcriptional control. Identification of RBPs bindi...

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Autores principales: Zhang, Jidong, Liu, Bo, Wang, Zhihan, Lehnert, Klaus, Gahegan, Mark
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9241231/
https://www.ncbi.nlm.nih.gov/pubmed/35768792
http://dx.doi.org/10.1186/s12859-022-04798-5
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author Zhang, Jidong
Liu, Bo
Wang, Zhihan
Lehnert, Klaus
Gahegan, Mark
author_facet Zhang, Jidong
Liu, Bo
Wang, Zhihan
Lehnert, Klaus
Gahegan, Mark
author_sort Zhang, Jidong
collection PubMed
description BACKGROUND: Addressing the laborious nature of traditional biological experiments by using an efficient computational approach to analyze RNA-binding proteins (RBPs) binding sites has always been a challenging task. RBPs play a vital role in post-transcriptional control. Identification of RBPs binding sites is a key step for the anatomy of the essential mechanism of gene regulation by controlling splicing, stability, localization and translation. Traditional methods for detecting RBPs binding sites are time-consuming and computationally-intensive. Recently, the computational method has been incorporated in researches of RBPs. Nevertheless, lots of them not only rely on the sequence data of RNA but also need additional data, for example the secondary structural data of RNA, to improve the performance of prediction, which needs the pre-work to prepare the learnable representation of structural data. RESULTS: To reduce the dependency of those pre-work, in this paper, we introduce DeepPN, a deep parallel neural network that is constructed with a convolutional neural network (CNN) and graph convolutional network (GCN) for detecting RBPs binding sites. It includes a two-layer CNN and GCN in parallel to extract the hidden features, followed by a fully connected layer to make the prediction. DeepPN discriminates the RBP binding sites on learnable representation of RNA sequences, which only uses the sequence data without using other data, for example the secondary or tertiary structure data of RNA. DeepPN is evaluated on 24 datasets of RBPs binding sites with other state-of-the-art methods. The results show that the performance of DeepPN is comparable to the published methods. CONCLUSION: The experimental results show that DeepPN can effectively capture potential hidden features in RBPs and use these features for effective prediction of binding sites.
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spelling pubmed-92412312022-06-30 DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites Zhang, Jidong Liu, Bo Wang, Zhihan Lehnert, Klaus Gahegan, Mark BMC Bioinformatics Research BACKGROUND: Addressing the laborious nature of traditional biological experiments by using an efficient computational approach to analyze RNA-binding proteins (RBPs) binding sites has always been a challenging task. RBPs play a vital role in post-transcriptional control. Identification of RBPs binding sites is a key step for the anatomy of the essential mechanism of gene regulation by controlling splicing, stability, localization and translation. Traditional methods for detecting RBPs binding sites are time-consuming and computationally-intensive. Recently, the computational method has been incorporated in researches of RBPs. Nevertheless, lots of them not only rely on the sequence data of RNA but also need additional data, for example the secondary structural data of RNA, to improve the performance of prediction, which needs the pre-work to prepare the learnable representation of structural data. RESULTS: To reduce the dependency of those pre-work, in this paper, we introduce DeepPN, a deep parallel neural network that is constructed with a convolutional neural network (CNN) and graph convolutional network (GCN) for detecting RBPs binding sites. It includes a two-layer CNN and GCN in parallel to extract the hidden features, followed by a fully connected layer to make the prediction. DeepPN discriminates the RBP binding sites on learnable representation of RNA sequences, which only uses the sequence data without using other data, for example the secondary or tertiary structure data of RNA. DeepPN is evaluated on 24 datasets of RBPs binding sites with other state-of-the-art methods. The results show that the performance of DeepPN is comparable to the published methods. CONCLUSION: The experimental results show that DeepPN can effectively capture potential hidden features in RBPs and use these features for effective prediction of binding sites. BioMed Central 2022-06-29 /pmc/articles/PMC9241231/ /pubmed/35768792 http://dx.doi.org/10.1186/s12859-022-04798-5 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Zhang, Jidong
Liu, Bo
Wang, Zhihan
Lehnert, Klaus
Gahegan, Mark
DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites
title DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites
title_full DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites
title_fullStr DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites
title_full_unstemmed DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites
title_short DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites
title_sort deeppn: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting rna-protein binding sites
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9241231/
https://www.ncbi.nlm.nih.gov/pubmed/35768792
http://dx.doi.org/10.1186/s12859-022-04798-5
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