The bioinformatics toolbox for circRNA discovery and analysis

Abstract Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types a...

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Published inBriefings in bioinformatics Vol. 22; no. 2; pp. 1706 - 1728
Main Authors Chen, Liang, Wang, Changliang, Sun, Huiyan, Wang, Juexin, Liang, Yanchun, Wang, Yan, Wong, Garry
Format Journal Article
LanguageEnglish
Published England Oxford University Press 22.03.2021
Oxford Publishing Limited (England)
Subjects
Annotations
Bioinformatics
Biomarkers
Data mining
Gene sequencing
Network analysis
Review
Ribonucleic acid
RNA
Splicing
text mining
circRNA
non-coding RNA
next generation sequencing
bioinformatics tools
disease biomarker
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Abstract Abstract Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.
AbstractList Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.
Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.
Abstract Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.
Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of linear RNA. Recent advances in sequencing technologies and bioinformatics tools have led directly to an ever-expanding field of types and biological functions of circRNAs. In parallel with technological developments, practical applications of circRNAs have arisen including their utilization as biomarkers of human disease. Currently, circRNA-associated bioinformatics tools can support projects including circRNA annotation, circRNA identification and network analysis of competing endogenous RNA (ceRNA). In this review, we collected about 100 circRNA-associated bioinformatics tools and summarized their current attributes and capabilities. We also performed network analysis and text mining on circRNA tool publications in order to reveal trends in their ongoing development.
Author Sun, Huiyan
Chen, Liang
Wang, Juexin
Wang, Changliang
Liang, Yanchun
Wang, Yan
Wong, Garry
AuthorAffiliation 2 Faculty of Health Sciences , University of Macau
5 College of Computer Science and Technology , Jilin University
4 Department of Electrical Engineering and Computer Science and Bond Life Science Center , University of Missouri
3 School of Artificial Intelligence , Jilin University
1 Department of Computer Science , Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University
AuthorAffiliation_xml – name: 1 Department of Computer Science , Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University
– name: 2 Faculty of Health Sciences , University of Macau
– name: 3 School of Artificial Intelligence , Jilin University
– name: 5 College of Computer Science and Technology , Jilin University
– name: 4 Department of Electrical Engineering and Computer Science and Bond Life Science Center , University of Missouri
Author_xml – sequence: 1
  givenname: Liang
  surname: Chen
  fullname: Chen, Liang
  email: ChenLiang@stu.edu.cn
  organization: Department of Computer Science, Key Laboratory of Intelligent Manufacturing Technology of Ministry of Education, Shantou University
– sequence: 2
  givenname: Changliang
  surname: Wang
  fullname: Wang, Changliang
  organization: Faculty of Health Sciences, University of Macau
– sequence: 3
  givenname: Huiyan
  surname: Sun
  fullname: Sun, Huiyan
  organization: School of Artificial Intelligence, Jilin University
– sequence: 4
  givenname: Juexin
  surname: Wang
  fullname: Wang, Juexin
  organization: Department of Electrical Engineering and Computer Science and Bond Life Science Center, University of Missouri
– sequence: 5
  givenname: Yanchun
  surname: Liang
  fullname: Liang, Yanchun
  email: ChenLiang@stu.edu.cn
  organization: College of Computer Science and Technology, Jilin University
– sequence: 6
  givenname: Yan
  surname: Wang
  fullname: Wang, Yan
  organization: College of Computer Science and Technology, Jilin University
– sequence: 7
  givenname: Garry
  surname: Wong
  fullname: Wong, Garry
  email: GarryGWong@um.edu.mo
  organization: Faculty of Health Sciences, University of Macau
BackLink https://www.ncbi.nlm.nih.gov/pubmed/32103237$$D View this record in MEDLINE/PubMed
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Issue 2
Keywords text mining
circRNA
non-coding RNA
next generation sequencing
bioinformatics tools
disease biomarker
Language English
License This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
http://creativecommons.org/licenses/by-nc/4.0
The Author(s) 2020. Published by Oxford University Press.
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content type line 14
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Liang Chen, Changliang Wang and Huiyan Sun contribute equally to this work.
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Snippet Abstract Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via...
Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of...
Circular RNAs (circRNAs) are a unique class of RNA molecule identified more than 40 years ago which are produced by a covalent linkage via back-splicing of...
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SubjectTerms Annotations
Bioinformatics
Biomarkers
Data mining
Gene sequencing
Network analysis
Review
Ribonucleic acid
RNA
Splicing
Title The bioinformatics toolbox for circRNA discovery and analysis
URI https://www.ncbi.nlm.nih.gov/pubmed/32103237
https://www.proquest.com/docview/2529968485
https://www.proquest.com/docview/2366648207
https://pubmed.ncbi.nlm.nih.gov/PMC7986655
Volume 22
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