Cargando…
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data
Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insi...
Autores principales: | , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2015
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565967/ https://www.ncbi.nlm.nih.gov/pubmed/26363020 http://dx.doi.org/10.1093/database/bav082 |
_version_ | 1782389654527410176 |
---|---|
author | Zhao, Zheng Bai, Jing Wu, Aiwei Wang, Yuan Zhang, Jinwen Wang, Zishan Li, Yongsheng Xu, Juan Li, Xia |
author_facet | Zhao, Zheng Bai, Jing Wu, Aiwei Wang, Yuan Zhang, Jinwen Wang, Zishan Li, Yongsheng Xu, Juan Li, Xia |
author_sort | Zhao, Zheng |
collection | PubMed |
description | Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/ |
format | Online Article Text |
id | pubmed-4565967 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-45659672015-09-15 Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data Zhao, Zheng Bai, Jing Wu, Aiwei Wang, Yuan Zhang, Jinwen Wang, Zishan Li, Yongsheng Xu, Juan Li, Xia Database (Oxford) Database Tool Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community. Database URL: http://www.bio-bigdata.com/Co-LncRNA/ Oxford University Press 2015-09-10 /pmc/articles/PMC4565967/ /pubmed/26363020 http://dx.doi.org/10.1093/database/bav082 Text en © The Author(s) 2015. Published by Oxford University Press. 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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Tool Zhao, Zheng Bai, Jing Wu, Aiwei Wang, Yuan Zhang, Jinwen Wang, Zishan Li, Yongsheng Xu, Juan Li, Xia Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data |
title | Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data |
title_full | Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data |
title_fullStr | Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data |
title_full_unstemmed | Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data |
title_short | Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data |
title_sort | co-lncrna: investigating the lncrna combinatorial effects in go annotations and kegg pathways based on human rna-seq data |
topic | Database Tool |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4565967/ https://www.ncbi.nlm.nih.gov/pubmed/26363020 http://dx.doi.org/10.1093/database/bav082 |
work_keys_str_mv | AT zhaozheng colncrnainvestigatingthelncrnacombinatorialeffectsingoannotationsandkeggpathwaysbasedonhumanrnaseqdata AT baijing colncrnainvestigatingthelncrnacombinatorialeffectsingoannotationsandkeggpathwaysbasedonhumanrnaseqdata AT wuaiwei colncrnainvestigatingthelncrnacombinatorialeffectsingoannotationsandkeggpathwaysbasedonhumanrnaseqdata AT wangyuan colncrnainvestigatingthelncrnacombinatorialeffectsingoannotationsandkeggpathwaysbasedonhumanrnaseqdata AT zhangjinwen colncrnainvestigatingthelncrnacombinatorialeffectsingoannotationsandkeggpathwaysbasedonhumanrnaseqdata AT wangzishan colncrnainvestigatingthelncrnacombinatorialeffectsingoannotationsandkeggpathwaysbasedonhumanrnaseqdata AT liyongsheng colncrnainvestigatingthelncrnacombinatorialeffectsingoannotationsandkeggpathwaysbasedonhumanrnaseqdata AT xujuan colncrnainvestigatingthelncrnacombinatorialeffectsingoannotationsandkeggpathwaysbasedonhumanrnaseqdata AT lixia colncrnainvestigatingthelncrnacombinatorialeffectsingoannotationsandkeggpathwaysbasedonhumanrnaseqdata |