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Database Commons - LNCipedia

LNCipedia

Citations: 168

z-index 17.47

Short name LNCipedia
Full name A comprehensive compendium of human long non-coding RNAs
Description Lncipedia.org is an integrated database of human annotated lncRNA transcripts obtained from different sources. In addition to basic transcript information and structure, several statistics are calculated for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites.
URL http://www.lncipedia.org/
Year founded 2013
Last update & version 12-09-16    v3.1
Availability Free to all users
University/Institution hosted Ghent University
Address Ghent 9000,Belgium
City Ghent
Province/State
Country/Region Belgium
Contact name Pieter Mestdagh
Contact email Pieter.Mestdagh@UGent.be
Data type(s)
Major organism(s)
Keyword(s)
  • human annotated lncRNA
  • miRNA binding site
  • protein coding potential
  • secondary structure information
Publication(s)
  • An update on LNCipedia: a database for annotated human lncRNA sequences. [PMID: 25378313]

    Pieter-Jan Volders, Kenneth Verheggen, Gerben Menschaert, Klaas Vandepoele, Lennart Martens, Jo Vandesompele, Pieter Mestdagh
    Nucleic acids research 2015:43(Database issue)
    33 Citations (Google Scholar as of 2015-12-27)

    Abstract: The human genome is pervasively transcribed, producing thousands of non-coding RNA transcripts. The majority of these transcripts are long non-coding RNAs (lncRNAs) and novel lncRNA genes are being identified at rapid pace. To streamline these efforts, we created LNCipedia, an online repository of lncRNA transcripts and annotation. Here, we present LNCipedia 3.0 (http://www.lncipedia.org), the latest version of the publicly available human lncRNA database. Compared to the previous version of LNCipedia, the database grew over five times in size, gaining over 90,000 new lncRNA transcripts. Assessment of the protein-coding potential of LNCipedia entries is improved with state-of-the art methods that include large-scale reprocessing of publicly available proteomics data. As a result, a high-confidence set of lncRNA transcripts with low coding potential is defined and made available for download. In addition, a tool to assess lncRNA gene conservation between human, mouse and zebrafish has been implemented. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  • LNCipedia: a database for annotated human lncRNA transcript sequences and structures. [PMID: 23042674]

    Pieter-Jan Volders, Kenny Helsens, Xiaowei Wang, Björn Menten, Lennart Martens, Kris Gevaert, Jo Vandesompele, Pieter Mestdagh
    Nucleic acids research 2013:41(Database issue)
    135 Citations (Google Scholar as of 2016-01-14)

    Abstract: Here, we present LNCipedia (http://www.lncipedia.org), a novel database for human long non-coding RNA (lncRNA) transcripts and genes. LncRNAs constitute a large and diverse class of non-coding RNA genes. Although several lncRNAs have been functionally annotated, the majority remains to be characterized. Different high-throughput methods to identify new lncRNAs (including RNA sequencing and annotation of chromatin-state maps) have been applied in various studies resulting in multiple unrelated lncRNA data sets. LNCipedia offers 21 488 annotated human lncRNA transcripts obtained from different sources. In addition to basic transcript information and gene structure, several statistics are determined for each entry in the database, such as secondary structure information, protein coding potential and microRNA binding sites. Our analyses suggest that, much like microRNAs, many lncRNAs have a significant secondary structure, in-line with their presumed association with proteins or protein complexes. Available literature on specific lncRNAs is linked, and users or authors can submit articles through a web interface. Protein coding potential is assessed by two different prediction algorithms: Coding Potential Calculator and HMMER. In addition, a novel strategy has been integrated for detecting potentially coding lncRNAs by automatically re-analysing the large body of publicly available mass spectrometry data in the PRIDE database. LNCipedia is publicly available and allows users to query and download lncRNA sequences and structures based on different search criteria. The database may serve as a resource to initiate small- and large-scale lncRNA studies. As an example, the LNCipedia content was used to develop a custom microarray for expression profiling of all available lncRNAs.

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200 OK2016-02-19
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200 OK2016-02-14
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200 OK2016-02-08
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200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
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200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

RNA
Homo sapiens
human annotated lncRNA miRNA binding site protein coding potential secondary structure information

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lina Ma [2016-05-30]
    • Chunlei Yu [2016-04-01]
    • Lina Ma [2016-01-14]
    • Lina Ma [2015-06-26]
Stats