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Nucleic Acids Res. 2017 Jan 4;45(D1):D790-D795. doi: 10.1093/nar/gkw1127. Epub 2016 Nov 29.

ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.

Author information

1
Faculty of Medicine in Galilee, Bar-Ilan University, Henrietta Szold 8, Safed 13195, Israel.
2
Faculty of Medicine in Galilee, Bar-Ilan University, Henrietta Szold 8, Safed 13195, Israel. Corresponding author: milana.morgenstern@biu.ac.il.

Abstract

Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922: chimeric transcripts along with 11 714: cancer breakpoints. In this latest version, we have included multiple cross-references to GeneCards, iHop, PubMed, NCBI, Ensembl, OMIM, RefSeq and the Mitelman collection for every entry in the 'Full Collection'. In addition, for every chimera, we have added a predicted Chimeric Protein-Protein Interaction (ChiPPI) network, which allows for easy visualization of protein partners of both parental and fusion proteins for all human chimeras. The database contains a comprehensive annotation for 34 922: chimeric transcripts from eight organisms, and includes the manual annotation of 200 sense-antiSense (SaS) chimeras. The current improvements in the content and functionality to the ChiTaRS database make it a central resource for the study of chimeric transcripts and fusion proteins.

PMID:
27899596
PMCID:
PMC5210585
DOI:
10.1093/nar/gkw1127
[Indexed for MEDLINE]
Free PMC Article

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