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An update on LNCipedia : a database for annotated human lncRNA sequences

Pieter-Jan Volders (UGent) , Kenneth Verheggen (UGent) , Gerben Menschaert (UGent) , Klaas Vandepoele (UGent) , Lennart Martens (UGent) , Jo Vandesompele (UGent) and Pieter Mestdagh (UGent)
(2015) NUCLEIC ACIDS RESEARCH. 43(D1). p.D174-D180
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Project
Bioinformatics: from nucleotids to networks (N2N)
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.
Keywords
RESOLUTION, CELLS, MASS-SPECTROMETRY, LONG NONCODING RNA, IDENTIFICATION, REVEALS, PROTEOMICS, INACTIVATION, DIFFERENTIATION, GENE

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Citation

Please use this url to cite or link to this publication:

Chicago
Volders, Pieter-Jan, Kenneth Verheggen, Gerben Menschaert, Klaas Vandepoele, Lennart Martens, Jo Vandesompele, and Pieter Mestdagh. 2015. “An Update on LNCipedia : a Database for Annotated Human lncRNA Sequences.” Nucleic Acids Research 43 (D1): D174–D180.
APA
Volders, P.-J., Verheggen, K., Menschaert, G., Vandepoele, K., Martens, L., Vandesompele, J., & Mestdagh, P. (2015). An update on LNCipedia : a database for annotated human lncRNA sequences. NUCLEIC ACIDS RESEARCH, 43(D1), D174–D180.
Vancouver
1.
Volders P-J, Verheggen K, Menschaert G, Vandepoele K, Martens L, Vandesompele J, et al. An update on LNCipedia : a database for annotated human lncRNA sequences. NUCLEIC ACIDS RESEARCH. 2015;43(D1):D174–D180.
MLA
Volders, Pieter-Jan, Kenneth Verheggen, Gerben Menschaert, et al. “An Update on LNCipedia : a Database for Annotated Human lncRNA Sequences.” NUCLEIC ACIDS RESEARCH 43.D1 (2015): D174–D180. Print.
@article{5847343,
  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.},
  author       = {Volders, Pieter-Jan and Verheggen, Kenneth and Menschaert, Gerben and Vandepoele, Klaas and Martens, Lennart and Vandesompele, Jo and Mestdagh, Pieter},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {RESOLUTION,CELLS,MASS-SPECTROMETRY,LONG NONCODING RNA,IDENTIFICATION,REVEALS,PROTEOMICS,INACTIVATION,DIFFERENTIATION,GENE},
  language     = {eng},
  number       = {D1},
  pages        = {D174--D180},
  title        = {An update on LNCipedia : a database for annotated human lncRNA sequences},
  url          = {http://dx.doi.org/10.1093/nar/gku1060},
  volume       = {43},
  year         = {2015},
}

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