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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...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2021
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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. |
format | Online Article Text |
id | pubmed-8728133 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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