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ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.

Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A - Nucleic Acids Res. (2014)

Bottom Line: 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 new database version collects more than 29,000 chimeric transcripts and indicates the expression and tissue specificity for 333 entries confirmed by RNA-seq reads mapping the chimeric junction sites.As a result, the ChiTaRS 2.1 collection of chimeras from eight organisms and human cancer breakpoints extends our understanding of the evolution of chimeric transcripts in eukaryotes as well as their functional role in carcinogenic processes.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.

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Related in: MedlinePlus

A new interface with enhanced query capacity and support information has been added to the ChiTaRS-2.1 database.
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Figure 3: A new interface with enhanced query capacity and support information has been added to the ChiTaRS-2.1 database.

Mentions: To improve the data access and analyses of the information on chimeric transcripts contained in ChiTaRS, a new interface with enhanced query capacity and support information have been added (Figure 3). Every ChiTaRS-2.1 entry is associated to a genomic position in the UCSC browser, which appears in a new pop-up window and includes downloadable files incorporating all the transcription start/stop sites, the genomic, chromosomal and strand location (Figure 3). Publications associated with each of the two genes in every chimera can be easily accessed using an automated PubMed search, and all the retrieved references can be downloaded using the ‘Save Text’ option (See ‘Full Collection’ and Figure 3). To improve the visual association of chimeric transcripts with gene function, we have added a link to the iHOP family (57–60) of web services (www.ihop-net.org/) for every gene in the ChiTaRS 2.1 database. The iHOP, Information Hyperlinked over Proteins (57), engine provides information on gene function, potential gene–gene relation in networks of genes, as an intuitive way of screening the millions of abstracts in PubMed for relevant publications (Figure 3). This improvement provides users with an easy means of exploring and combining information for each parental gene of a chimera.


ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.

Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A - Nucleic Acids Res. (2014)

A new interface with enhanced query capacity and support information has been added to the ChiTaRS-2.1 database.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383979&req=5

Figure 3: A new interface with enhanced query capacity and support information has been added to the ChiTaRS-2.1 database.
Mentions: To improve the data access and analyses of the information on chimeric transcripts contained in ChiTaRS, a new interface with enhanced query capacity and support information have been added (Figure 3). Every ChiTaRS-2.1 entry is associated to a genomic position in the UCSC browser, which appears in a new pop-up window and includes downloadable files incorporating all the transcription start/stop sites, the genomic, chromosomal and strand location (Figure 3). Publications associated with each of the two genes in every chimera can be easily accessed using an automated PubMed search, and all the retrieved references can be downloaded using the ‘Save Text’ option (See ‘Full Collection’ and Figure 3). To improve the visual association of chimeric transcripts with gene function, we have added a link to the iHOP family (57–60) of web services (www.ihop-net.org/) for every gene in the ChiTaRS 2.1 database. The iHOP, Information Hyperlinked over Proteins (57), engine provides information on gene function, potential gene–gene relation in networks of genes, as an intuitive way of screening the millions of abstracts in PubMed for relevant publications (Figure 3). This improvement provides users with an easy means of exploring and combining information for each parental gene of a chimera.

Bottom Line: 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 new database version collects more than 29,000 chimeric transcripts and indicates the expression and tissue specificity for 333 entries confirmed by RNA-seq reads mapping the chimeric junction sites.As a result, the ChiTaRS 2.1 collection of chimeras from eight organisms and human cancer breakpoints extends our understanding of the evolution of chimeric transcripts in eukaryotes as well as their functional role in carcinogenic processes.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.

Show MeSH
Related in: MedlinePlus