title: ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.
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.
authors.affiliation: Faculty of Medicine in Galilee, Bar-Ilan University, Henrietta Szold 8, Safed 13195, Israel.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Gorohovski
authors.affiliation: Faculty of Medicine in Galilee, Bar-Ilan University, Henrietta Szold 8, Safed 13195, Israel.
authors.forename: Somnath
authors.initials: S
authors.lastname: Tagore
authors.affiliation: Faculty of Medicine in Galilee, Bar-Ilan University, Henrietta Szold 8, Safed 13195, Israel.
authors.forename: Vikrant
authors.initials: V
authors.lastname: Palande
authors.affiliation: Faculty of Medicine in Galilee, Bar-Ilan University, Henrietta Szold 8, Safed 13195, Israel.
authors.forename: Assaf
authors.initials: A
authors.lastname: Malka
authors.affiliation: Faculty of Medicine in Galilee, Bar-Ilan University, Henrietta Szold 8, Safed 13195, Israel.
authors.forename: Dorith
authors.initials: D
authors.lastname: Raviv-Shay
authors.affiliation: Faculty of Medicine in Galilee, Bar-Ilan University, Henrietta Szold 8, Safed 13195, Israel. Corresponding author: milana.morgenstern@biu.ac.il.
authors.forename: Milana
authors.initials: M
authors.lastname: Frenkel-Morgenstern
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D030541:Databases, Genetic; D006801:Humans; D025941:Protein Interaction Mapping / Q000379:methods*; D060066:Protein Interaction Maps; D012313:RNA; D020040:Trans-Splicing; D014158:Transcription, Genetic; D014178:Translocation, Genetic; D064878:Web Browser
chemical_list: D012313:RNA