期刊
NUCLEIC ACIDS RESEARCH
卷 41, 期 D1, 页码 D142-D151出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gks1041
关键词
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资金
- Miguel Servet (FIS) grant
- Obra Social laCaixa grant
- National Science Foundation ABI [0743097]
- NHGRI-NIH ENCODE [HG00455-04]
- Blueprint European Union [282510]
- Spanish Government [BIO2007-66855]
- Spanish National Bioinformatics Institute (INB-ISCIII), Genecode/ENCODE NHGRI-NIH [HG00455-04]
- Plan Cancer, ERC Advanced Grant Sisyphe, Investissements d'avenir en Bioinformatique
- Div Of Biological Infrastructure
- Direct For Biological Sciences [0743097] Funding Source: National Science Foundation
Chimeric RNAs that comprise two or more different transcripts have been identified in many cancers and among the Expressed Sequence Tags (ESTs) isolated from different organisms; they might represent functional proteins and produce different disease phenotypes. The ChiTaRS database of Chimeric Transcripts and RNA-Sequencing data (http://chitars.bioinfo.cnio.es/) collects more than 16 000 chimeric RNAs from humans, mice and fruit flies, 233 chimeras confirmed by RNA-seq reads and similar to 2000 cancer breakpoints. The database indicates the expression and tissue specificity of these chimeras, as confirmed by RNA-seq data, and it includes mass spectrometry results for some human entries at their junctions. Moreover, the database has advanced features to analyze junction consistency and to rank chimeras based on the evidence of repeated junction sites. Finally, 'Junction Search' screens through the RNA-seq reads found at the chimeras' junction sites to identify putative junctions in novel sequences entered by users. Thus, ChiTaRS is an extensive catalog of human, mouse and fruit fly chimeras that will extend our understanding of the evolution of chimeric transcripts in eukaryotes and can be advantageous in the analysis of human cancer breakpoints.
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