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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

Milana Frenkel-Morgenstern, Alessandro Gorohovski, Dunja Vucenovic, Lorena Maestre, Alfonso Valencia
2014 Nucleic Acids Research  
The ChiTaRS 2.1 database of chimeric transcripts and RNA-Seq data (http: //chitars.bioinfo.cnio.es/) is the second version of the ChiTaRS database and includes improvements in content and functionality  ...  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  ...  manual verification of all the cancer breakpoints in ChiTaRS-2.1, the ACGT Inc. for the RT-qPCR, cloning and sequencing experiments, the Genomics Unit at CNIO for RNA extractions, library preparation and  ... 
doi:10.1093/nar/gku1199 pmid:25414346 pmcid:PMC4383979 fatcat:rbhpz7eslzhjvkjlz7uwdlmav4

ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps

2019 Nucleic Acids Research  
It extends our understanding of the evolution of chimeric transcripts in eukaryotes and contributes to the analysis of 3D genome conformational changes and the functional role of chimeras in the etiopathogenesis  ...  Thus, this improved version is an extensive catalogue of chimeras from multiple species.  ...  ACKNOWLEDGEMENTS The authors would like to thank MPLabs Ltd for their efforts in making ChiTaRS 5.0 a reality through website design and back-end support.  ... 
doi:10.1093/nar/gkz1025 pmid:31747015 pmcid:PMC7145514 fatcat:bjfnkwc5xvczdchrfiqfq5syky

A liquid biopsy platform for detecting gene-gene fusions as glioma diagnostic biomarkers and drug targets [article]

Vikrant Palande, Rajesh Detroja, Alessandro Gorohovski, Rainer Glass, Charlotte Flueh, Marina Kurtz, Shira Perez, Dorith Raviv Shay, Tali Siegal, Milana Frenkel-Morgenstern
2020 bioRxiv   pre-print
Point mutations found in glioma tissue biopsies were also found in the cfDNA samples (95% identity). Finally, we identified novel chimeric genes (gene-gene fusions) in both tumour and cfDNA samples.  ...  Glioblastoma multiforme (GBM) is the most common type of glioma, and is uniformly fatal. The median survival of treated GBM patients is 12-15 months.  ...  ChiTaRS 2.1-an 555 improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric 556 RNA transcripts. Nucleic Acids Res (2014) doi:10.1093/nar/gku1199. 557 110.  ... 
doi:10.1101/2020.02.25.963975 fatcat:aut5j2efl5cylogjlyf5u7nope