Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions

Abstract Circular RNAs, a family of covalently circularized RNAs with tissue-specific expression, were recently demonstrated to play important roles in mammalian biology. Regardless of extensive research to predict, quantify, and annotate circRNAs, our understanding of their functions is still in it...

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Autores principales:	Jacob Cardenas, Uthra Balaji, Jinghua Gu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/a71efba5d4be4a078814243fe871b0e6
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spelling	oai:doaj.org-article:a71efba5d4be4a078814243fe871b0e62021-12-02T11:57:58ZCerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions10.1038/s41598-020-78469-x2045-2322https://doaj.org/article/a71efba5d4be4a078814243fe871b0e62020-12-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-78469-xhttps://doaj.org/toc/2045-2322Abstract Circular RNAs, a family of covalently circularized RNAs with tissue-specific expression, were recently demonstrated to play important roles in mammalian biology. Regardless of extensive research to predict, quantify, and annotate circRNAs, our understanding of their functions is still in its infancy. In this study, we developed a novel computational tool: Competing Endogenous RNA for INtegrative Annotations (Cerina), to predict biological functions of circRNAs based on the competing endogenous RNA model. Pareto Frontier Analysis was employed to integrate ENCODE mRNA/miRNA data with predicted microRNA response elements to prioritize tissue-specific ceRNA interactions. Using data from several circRNA-disease databases, we demonstrated that Cerina significantly improved the functional relevance of the prioritized ceRNA interactions by several folds, in terms of precision and recall. Proof-of-concept studies on human cancers and cardiovascular diseases further showcased the efficacy of Cerina on predicting potential circRNA functions in human diseases.Jacob CardenasUthra BalajiJinghua GuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-14 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jacob Cardenas Uthra Balaji Jinghua Gu Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
description	Abstract Circular RNAs, a family of covalently circularized RNAs with tissue-specific expression, were recently demonstrated to play important roles in mammalian biology. Regardless of extensive research to predict, quantify, and annotate circRNAs, our understanding of their functions is still in its infancy. In this study, we developed a novel computational tool: Competing Endogenous RNA for INtegrative Annotations (Cerina), to predict biological functions of circRNAs based on the competing endogenous RNA model. Pareto Frontier Analysis was employed to integrate ENCODE mRNA/miRNA data with predicted microRNA response elements to prioritize tissue-specific ceRNA interactions. Using data from several circRNA-disease databases, we demonstrated that Cerina significantly improved the functional relevance of the prioritized ceRNA interactions by several folds, in terms of precision and recall. Proof-of-concept studies on human cancers and cardiovascular diseases further showcased the efficacy of Cerina on predicting potential circRNA functions in human diseases.
format	article
author	Jacob Cardenas Uthra Balaji Jinghua Gu
author_facet	Jacob Cardenas Uthra Balaji Jinghua Gu
author_sort	Jacob Cardenas
title	Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
title_short	Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
title_full	Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
title_fullStr	Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
title_full_unstemmed	Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
title_sort	cerina: systematic circrna functional annotation based on integrative analysis of cerna interactions
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/a71efba5d4be4a078814243fe871b0e6
work_keys_str_mv	AT jacobcardenas cerinasystematiccircrnafunctionalannotationbasedonintegrativeanalysisofcernainteractions AT uthrabalaji cerinasystematiccircrnafunctionalannotationbasedonintegrativeanalysisofcernainteractions AT jinghuagu cerinasystematiccircrnafunctionalannotationbasedonintegrativeanalysisofcernainteractions
_version_	1718394767183708160

Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions

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