LNCipedia: a database for annotated human lncRNA transcript sequences and structures
| Autor: | Jo Vandesompele, Björn Menten, Lennart Martens, Kenny Helsens, Xiaowei Wang, Pieter-Jan Volders, Kris Gevaert, Pieter Mestdagh |
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| Rok vydání: | 2012 |
| Předmět: |
Biology
computer.software_genre Transcriptome 03 medical and health sciences Annotation 0302 clinical medicine REVEALS microRNA Genetics Humans Gene 030304 developmental biology Internet 0303 health sciences Database LONG NONCODING RNA Proteins Biology and Life Sciences RNA Molecular Sequence Annotation Articles TANDEM MASS-SPECTRA GENE Long non-coding RNA Gene expression profiling DIFFERENTIATION 030220 oncology & carcinogenesis RNA Long Noncoding Databases Nucleic Acid computer Software |
| Zdroj: | NUCLEIC ACIDS RESEARCH Nucleic Acids Research |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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