LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning

Bioinformatics
Cheng YangHuaiqiu Zhu

Abstract

To characterize long non-coding RNAs (lncRNAs), both identifying and functionally annotating them are essential to be addressed. Moreover, a comprehensive construction for lncRNA annotation is desired to facilitate the research in the field. We present LncADeep, a novel lncRNA identification and functional annotation tool. For lncRNA identification, LncADeep integrates intrinsic and homology features into a deep belief network and constructs models targeting both full- and partial-length transcripts. For functional annotation, LncADeep predicts a lncRNA's interacting proteins based on deep neural networks, using both sequence and structure information. Furthermore, LncADeep integrates KEGG and Reactome pathway enrichment analysis and functional module detection with the predicted interacting proteins, and provides the enriched pathways and functional modules as functional annotations for lncRNAs. Test results show that LncADeep outperforms state-of-the-art tools, both for lncRNA identification and lncRNA-protein interaction prediction, and then presents a functional interpretation. We expect that LncADeep can contribute to identifying and annotating novel lncRNAs. LncADeep is freely available for academic use at http://cqb.pku....Continue Reading

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Citations

Jun 4, 2019·Cells·Jael Sanyanda WekesaJun Meng
Nov 5, 2019·Journal of Cellular Biochemistry·Zun-Ping KeJian Sun
May 15, 2020·Briefings in Bioinformatics·Ye WangLi Chen
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May 11, 2021·Briefings in Bioinformatics·Dalwinder SinghJoy Roy
Jun 6, 2021·BMC Genomics·Sébastien RiquierThérèse Commes
Apr 7, 2021·Briefings in Bioinformatics·Zi-Ang ShenPu-Feng Du
Aug 10, 2021·Briefings in Bioinformatics·Hansi ZhengHaiyan Hu
Aug 28, 2021·International Journal of Molecular Sciences·Muhammad Nabeel AsimSheraz Ahmed
Oct 31, 2020·Computers in Biology and Medicine·Yashpal RamakrishnaiahSonika Tyagi

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