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lncRNAfunc: a knowledgebase of lncRNA function in human cancer

The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we b...

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Detalles Bibliográficos
Autores principales: Yang, Mengyuan, Lu, Huifen, Liu, Jiajia, Wu, Sijia, Kim, Pora, Zhou, Xiaobo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728133/
https://www.ncbi.nlm.nih.gov/pubmed/34791419
http://dx.doi.org/10.1093/nar/gkab1035
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author Yang, Mengyuan
Lu, Huifen
Liu, Jiajia
Wu, Sijia
Kim, Pora
Zhou, Xiaobo
author_facet Yang, Mengyuan
Lu, Huifen
Liu, Jiajia
Wu, Sijia
Kim, Pora
Zhou, Xiaobo
author_sort Yang, Mengyuan
collection PubMed
description The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we built lncRNAfunc, a knowledgebase of lncRNA function in human cancer at https://ccsm.uth.edu/lncRNAfunc, aiming to provide a resource and reference for providing therapeutically targetable lncRNAs and intensive interaction regulations. To do this, we collected 15 900 lncRNAs across 33 cancer types from TCGA. For individual lncRNAs, we performed multiple interaction analyses of different biomolecules including DNA, RNA, and protein levels. Our intensive studies of lncRNAs provide diverse potential mechanisms of lncRNAs that regulate gene expression through binding enhancers and 3′-UTRs of genes, competing for miRNA binding sites with mRNAs, recruiting the transcription factors to gene promoters. Furthermore, we investigated lncRNAs that potentially affect the alternative splicing events through interacting with RNA binding Proteins. We also performed multiple functional annotations including cancer stage-associated lncRNAs, RNA A-to-I editing event-associated lncRNAs, and lncRNA expression quantitative trait loci. lncRNAfunc is a unique resource for cancer research communities to help better understand potential lncRNA regulations and therapeutic lncRNA targets.
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spelling pubmed-87281332022-01-05 lncRNAfunc: a knowledgebase of lncRNA function in human cancer Yang, Mengyuan Lu, Huifen Liu, Jiajia Wu, Sijia Kim, Pora Zhou, Xiaobo Nucleic Acids Res Database Issue The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we built lncRNAfunc, a knowledgebase of lncRNA function in human cancer at https://ccsm.uth.edu/lncRNAfunc, aiming to provide a resource and reference for providing therapeutically targetable lncRNAs and intensive interaction regulations. To do this, we collected 15 900 lncRNAs across 33 cancer types from TCGA. For individual lncRNAs, we performed multiple interaction analyses of different biomolecules including DNA, RNA, and protein levels. Our intensive studies of lncRNAs provide diverse potential mechanisms of lncRNAs that regulate gene expression through binding enhancers and 3′-UTRs of genes, competing for miRNA binding sites with mRNAs, recruiting the transcription factors to gene promoters. Furthermore, we investigated lncRNAs that potentially affect the alternative splicing events through interacting with RNA binding Proteins. We also performed multiple functional annotations including cancer stage-associated lncRNAs, RNA A-to-I editing event-associated lncRNAs, and lncRNA expression quantitative trait loci. lncRNAfunc is a unique resource for cancer research communities to help better understand potential lncRNA regulations and therapeutic lncRNA targets. Oxford University Press 2021-11-17 /pmc/articles/PMC8728133/ /pubmed/34791419 http://dx.doi.org/10.1093/nar/gkab1035 Text en © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Yang, Mengyuan
Lu, Huifen
Liu, Jiajia
Wu, Sijia
Kim, Pora
Zhou, Xiaobo
lncRNAfunc: a knowledgebase of lncRNA function in human cancer
title lncRNAfunc: a knowledgebase of lncRNA function in human cancer
title_full lncRNAfunc: a knowledgebase of lncRNA function in human cancer
title_fullStr lncRNAfunc: a knowledgebase of lncRNA function in human cancer
title_full_unstemmed lncRNAfunc: a knowledgebase of lncRNA function in human cancer
title_short lncRNAfunc: a knowledgebase of lncRNA function in human cancer
title_sort lncrnafunc: a knowledgebase of lncrna function in human cancer
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728133/
https://www.ncbi.nlm.nih.gov/pubmed/34791419
http://dx.doi.org/10.1093/nar/gkab1035
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