LncRBase: An Enriched Resource for lncRNA Information

Long noncoding RNAs (lncRNAs) are noncoding transcripts longer than 200 nucleotides, which show evidence of pervasive transcription and participate in a plethora of cellular regulatory processes. Although several noncoding transcripts have been functionally annotated as lncRNAs within the genome, no...

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Main Authors:	Chakraborty, Sohini, Deb, Aritra, Maji, Ranjan Kumar, Saha, Sudipto, Ghosh, Zhumur
Format:	Online
Language:	English
Published:	Public Library of Science 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169474/

id	pubmed-4169474
recordtype	oai_dc
spelling	pubmed-41694742014-09-22 LncRBase: An Enriched Resource for lncRNA Information Chakraborty, Sohini Deb, Aritra Maji, Ranjan Kumar Saha, Sudipto Ghosh, Zhumur Research Article Long noncoding RNAs (lncRNAs) are noncoding transcripts longer than 200 nucleotides, which show evidence of pervasive transcription and participate in a plethora of cellular regulatory processes. Although several noncoding transcripts have been functionally annotated as lncRNAs within the genome, not all have been proven to fulfill the criteria for a functional regulator and further analyses have to be done in order to include them in a functional cohort. LncRNAs are being classified and reclassified in an ongoing annotation process, and the challenge is fraught with ambiguity, as newer evidences of their biogenesis and functional implication come into light. In our effort to understand the complexity of this still enigmatic biomolecule, we have developed a new database entitled “LncRBase” where we have classified and characterized lncRNAs in human and mouse. It is an extensive resource of human and mouse lncRNA transcripts belonging to fourteen distinct subtypes, with a total of 83,201 entries for mouse and 133,361 entries for human: among these, we have newly annotated 8,507 mouse and 14,813 human non coding RNA transcripts (from UCSC and H-InvDB 8.0) as lncRNAs. We have especially considered protein coding gene loci which act as hosts for non coding transcripts. LncRBase includes different lncRNA transcript variants of protein coding genes within LncRBase. LncRBase provides information about the genomic context of different lncRNA subtypes, their interaction with small non coding RNAs (ncRNAs) viz. piwi interacting RNAs (piRNAs) and microRNAs (miRNAs) and their mode of regulation, via association with diverse other genomic elements. Adequate knowledge about genomic origin and molecular features of lncRNAs is essential to understand their functional and behavioral complexities. Overall, LncRBase provides a thorough study on various aspects of lncRNA origin and function and a user-friendly interface to search for lncRNA information. LncRBase is available at http://bicresources.jcbose.ac.in/zhumur/lncrbase. Public Library of Science 2014-09-18 /pmc/articles/PMC4169474/ /pubmed/25233092 http://dx.doi.org/10.1371/journal.pone.0108010 Text en © 2014 Chakraborty et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Chakraborty, Sohini Deb, Aritra Maji, Ranjan Kumar Saha, Sudipto Ghosh, Zhumur
spellingShingle	Chakraborty, Sohini Deb, Aritra Maji, Ranjan Kumar Saha, Sudipto Ghosh, Zhumur LncRBase: An Enriched Resource for lncRNA Information
author_facet	Chakraborty, Sohini Deb, Aritra Maji, Ranjan Kumar Saha, Sudipto Ghosh, Zhumur
author_sort	Chakraborty, Sohini
title	LncRBase: An Enriched Resource for lncRNA Information
title_short	LncRBase: An Enriched Resource for lncRNA Information
title_full	LncRBase: An Enriched Resource for lncRNA Information
title_fullStr	LncRBase: An Enriched Resource for lncRNA Information
title_full_unstemmed	LncRBase: An Enriched Resource for lncRNA Information
title_sort	lncrbase: an enriched resource for lncrna information
description	Long noncoding RNAs (lncRNAs) are noncoding transcripts longer than 200 nucleotides, which show evidence of pervasive transcription and participate in a plethora of cellular regulatory processes. Although several noncoding transcripts have been functionally annotated as lncRNAs within the genome, not all have been proven to fulfill the criteria for a functional regulator and further analyses have to be done in order to include them in a functional cohort. LncRNAs are being classified and reclassified in an ongoing annotation process, and the challenge is fraught with ambiguity, as newer evidences of their biogenesis and functional implication come into light. In our effort to understand the complexity of this still enigmatic biomolecule, we have developed a new database entitled “LncRBase” where we have classified and characterized lncRNAs in human and mouse. It is an extensive resource of human and mouse lncRNA transcripts belonging to fourteen distinct subtypes, with a total of 83,201 entries for mouse and 133,361 entries for human: among these, we have newly annotated 8,507 mouse and 14,813 human non coding RNA transcripts (from UCSC and H-InvDB 8.0) as lncRNAs. We have especially considered protein coding gene loci which act as hosts for non coding transcripts. LncRBase includes different lncRNA transcript variants of protein coding genes within LncRBase. LncRBase provides information about the genomic context of different lncRNA subtypes, their interaction with small non coding RNAs (ncRNAs) viz. piwi interacting RNAs (piRNAs) and microRNAs (miRNAs) and their mode of regulation, via association with diverse other genomic elements. Adequate knowledge about genomic origin and molecular features of lncRNAs is essential to understand their functional and behavioral complexities. Overall, LncRBase provides a thorough study on various aspects of lncRNA origin and function and a user-friendly interface to search for lncRNA information. LncRBase is available at http://bicresources.jcbose.ac.in/zhumur/lncrbase.
publisher	Public Library of Science
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169474/
_version_	1613135605677424640

LncRBase: An Enriched Resource for lncRNA Information

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