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LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data

BACKGROUND: The GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes. However, the vast majority of them remain to be functionally characterized. Computational investigation of potential functions of human lncRNA genes is helpful to guide further experimental studies on...

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Autores principales: Jiang, Qinghua, Ma, Rui, Wang, Jixuan, Wu, Xiaoliang, Jin, Shuilin, Peng, Jiajie, Tan, Renjie, Zhang, Tianjiao, Li, Yu, Wang, Yadong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331805/
https://www.ncbi.nlm.nih.gov/pubmed/25707511
http://dx.doi.org/10.1186/1471-2164-16-S3-S2
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author Jiang, Qinghua
Ma, Rui
Wang, Jixuan
Wu, Xiaoliang
Jin, Shuilin
Peng, Jiajie
Tan, Renjie
Zhang, Tianjiao
Li, Yu
Wang, Yadong
author_facet Jiang, Qinghua
Ma, Rui
Wang, Jixuan
Wu, Xiaoliang
Jin, Shuilin
Peng, Jiajie
Tan, Renjie
Zhang, Tianjiao
Li, Yu
Wang, Yadong
author_sort Jiang, Qinghua
collection PubMed
description BACKGROUND: The GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes. However, the vast majority of them remain to be functionally characterized. Computational investigation of potential functions of human lncRNA genes is helpful to guide further experimental studies on lncRNAs. RESULTS: In this study, based on expression correlation between lncRNAs and protein-coding genes across 19 human normal tissues, we used the hypergeometric test to functionally annotate a single lncRNA or a set of lncRNAs with significantly enriched functional terms among the protein-coding genes that are significantly co-expressed with the lncRNA(s). The functional terms include all nodes in the Gene Ontology (GO) and 4,380 human biological pathways collected from 12 pathway databases. We successfully mapped 9,625 human lncRNA genes to GO terms and biological pathways, and then developed the first ontology-driven user-friendly web interface named lncRNA2Function, which enables researchers to browse the lncRNAs associated with a specific functional term, the functional terms associated with a specific lncRNA, or to assign functional terms to a set of human lncRNA genes, such as a cluster of co-expressed lncRNAs. The lncRNA2Function is freely available at http://mlg.hit.edu.cn/lncrna2function. CONCLUSIONS: The LncRNA2Function is an important resource for further investigating the functions of a single human lncRNA, or functionally annotating a set of human lncRNAs of interest.
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spelling pubmed-43318052015-03-19 LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data Jiang, Qinghua Ma, Rui Wang, Jixuan Wu, Xiaoliang Jin, Shuilin Peng, Jiajie Tan, Renjie Zhang, Tianjiao Li, Yu Wang, Yadong BMC Genomics Proceedings BACKGROUND: The GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes. However, the vast majority of them remain to be functionally characterized. Computational investigation of potential functions of human lncRNA genes is helpful to guide further experimental studies on lncRNAs. RESULTS: In this study, based on expression correlation between lncRNAs and protein-coding genes across 19 human normal tissues, we used the hypergeometric test to functionally annotate a single lncRNA or a set of lncRNAs with significantly enriched functional terms among the protein-coding genes that are significantly co-expressed with the lncRNA(s). The functional terms include all nodes in the Gene Ontology (GO) and 4,380 human biological pathways collected from 12 pathway databases. We successfully mapped 9,625 human lncRNA genes to GO terms and biological pathways, and then developed the first ontology-driven user-friendly web interface named lncRNA2Function, which enables researchers to browse the lncRNAs associated with a specific functional term, the functional terms associated with a specific lncRNA, or to assign functional terms to a set of human lncRNA genes, such as a cluster of co-expressed lncRNAs. The lncRNA2Function is freely available at http://mlg.hit.edu.cn/lncrna2function. CONCLUSIONS: The LncRNA2Function is an important resource for further investigating the functions of a single human lncRNA, or functionally annotating a set of human lncRNAs of interest. BioMed Central 2015-01-29 /pmc/articles/PMC4331805/ /pubmed/25707511 http://dx.doi.org/10.1186/1471-2164-16-S3-S2 Text en Copyright © 2015 Jiang et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Proceedings
Jiang, Qinghua
Ma, Rui
Wang, Jixuan
Wu, Xiaoliang
Jin, Shuilin
Peng, Jiajie
Tan, Renjie
Zhang, Tianjiao
Li, Yu
Wang, Yadong
LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
title LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
title_full LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
title_fullStr LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
title_full_unstemmed LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
title_short LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data
title_sort lncrna2function: a comprehensive resource for functional investigation of human lncrnas based on rna-seq data
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331805/
https://www.ncbi.nlm.nih.gov/pubmed/25707511
http://dx.doi.org/10.1186/1471-2164-16-S3-S2
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