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作者:

Huang, Xiaoqian (Huang, Xiaoqian.) | Shi, Yi (Shi, Yi.) | Yan, Jing (Yan, Jing.) | Qu, Wenyan (Qu, Wenyan.) | Li, Xiaoyi (Li, Xiaoyi.) | Tan, Jianjun (Tan, Jianjun.)

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EI Scopus SCIE

摘要:

Long non-coding RNAs (LncRNAs) play important roles in a series of life activities, and they function primarily with proteins. The wet experimental-based methods in lncRNA-protein interactions (lncRPIs) study are timeconsuming and expensive. In this study, we propose for the first time a novel feature fusion method, the LPICSFFR, to train and predict LncRPIs based on a Convolutional Neural Network (CNN) with feature reuse and serial fusion in sequences, secondary structures, and physicochemical properties of proteins and lncRNAs. The experimental results indicate that LPI-CSFFR achieves excellent performance on the datasets RPI1460 and RPI1807 with an accuracy of 83.7 % and 98.1 %, respectively. We further compare LPI-CSFFR with the state-ofthe-art existing methods on the same benchmark datasets to evaluate the performance. In addition, to test the generalization performance of the model, we independently test sample pairs of five model organisms, where Mus musculus are the highest prediction accuracy of 99.5 %, and we find multiple hotspot proteins after constructing an interaction network. Finally, we test the predictive power of the LPI-CSFFR for sample pairs with unknown interactions. The results indicate that LPI-CSFFR is promising for predicting potential LncRPIs. The relevant source code and the data used in this study are available at https://github.com/JianjunTan-Beijing/LPICSFFR.

关键词:

LncRNA-protein interactions Convolution neural network Serial fusion Feature reuse

作者机构:

  • [ 1 ] [Huang, Xiaoqian]Beijing Univ Technol, Fac Environm & Life, Dept Biomed Engn, Beijing Int Sci & Technol Cooperat Base Intelligen, Beijing 100124, Peoples R China
  • [ 2 ] [Shi, Yi]Beijing Univ Technol, Fac Environm & Life, Dept Biomed Engn, Beijing Int Sci & Technol Cooperat Base Intelligen, Beijing 100124, Peoples R China
  • [ 3 ] [Yan, Jing]Beijing Univ Technol, Fac Environm & Life, Dept Biomed Engn, Beijing Int Sci & Technol Cooperat Base Intelligen, Beijing 100124, Peoples R China
  • [ 4 ] [Qu, Wenyan]Beijing Univ Technol, Fac Environm & Life, Dept Biomed Engn, Beijing Int Sci & Technol Cooperat Base Intelligen, Beijing 100124, Peoples R China
  • [ 5 ] [Li, Xiaoyi]Beijing Univ Technol, Fac Environm & Life, Dept Biomed Engn, Beijing Int Sci & Technol Cooperat Base Intelligen, Beijing 100124, Peoples R China
  • [ 6 ] [Tan, Jianjun]Beijing Univ Technol, Fac Environm & Life, Dept Biomed Engn, Beijing Int Sci & Technol Cooperat Base Intelligen, Beijing 100124, Peoples R China

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来源 :

COMPUTATIONAL BIOLOGY AND CHEMISTRY

ISSN: 1476-9271

年份: 2022

卷: 99

3 . 1

JCR@2022

3 . 1 0 0

JCR@2022

ESI学科: COMPUTER SCIENCE;

ESI高被引阀值:46

JCR分区:2

中科院分区:3

被引次数:

WoS核心集被引频次: 6

SCOPUS被引频次: 5

ESI高被引论文在榜: 0 展开所有

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中文被引频次:

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