An update on LNCipedia: a database for annotated human lncRNA sequences.
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.
Center for Medical Genetics, Ghent University, Ghent 9000, Belgium.
Pieter-Jan
PJ
Volders
Department of Medical Protein Research, VIB, Ghent 9000, Belgium Department of Biochemistry, Ghent University, Ghent 9000 Belgium.
Kenneth
K
Verheggen
Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent 9000, Belgium.
Gerben
G
Menschaert
Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent 9000, Belgium Department of Plant Systems Biology, VIB, Ghent 9000, Belgium.
Klaas
K
Vandepoele
Department of Medical Protein Research, VIB, Ghent 9000, Belgium Department of Biochemistry, Ghent University, Ghent 9000 Belgium.
Lennart
L
Martens
Center for Medical Genetics, Ghent University, Ghent 9000, Belgium.
Jo
J
Vandesompele
Center for Medical Genetics, Ghent University, Ghent 9000, Belgium Pieter.Mestdagh@UGent.be.
Pieter
P
Mestdagh
D000818:Animals; D030561:Databases, Nucleic Acid; D057809:HEK293 Cells; D006801:Humans; D020407:Internet; D051379:Mice; D058977:Molecular Sequence Annotation; D011506:Proteins / Q000235:genetics; D062085:RNA, Long Noncoding / Q000737:chemistry* / Q000235:genetics; D017423:Sequence Analysis, RNA; D015027:Zebrafish / Q000235:genetics
D011506:Proteins; D062085:RNA, Long Noncoding