ArticleNucleic acids research2015
ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Identification of Cross-Strand Chimeric RNAs with cscMap.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computational models for pan-cancer classification based on multi-omics data.Frontiers in genetics · 2025Review
- Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae).Scientific reports · 2023Article
- Detection of gene mutations and gene-gene fusions in circulating cell-free DNA of glioblastoma patients: an avenue for clinically relevant diagnostic analysis.Molecular oncology · 2022Article
- ChiTaH: a fast and accurate tool for identifying known human chimeric sequences from high-throughput sequencing data.NAR genomics and bioinformatics · 2021Article
- Comparative study of bioinformatic tools for the identification of chimeric RNAs from RNA Sequencing.RNA biology · 2021Article
- Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells.NAR genomics and bioinformatics · 2021Article
- Identification of the cross-strand chimeric RNAs generated by fusions of bi-directional transcripts.Nature communications · 2021Article
- ChiTaRS 5.0: the comprehensive database of chimeric transcripts matched with druggable fusions and 3D chromatin maps.Nucleic acids research · 2020Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
- ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.Nucleic acids research · 2017Article
- ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.Nucleic acids research · 2017Article
- ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.Nucleic acids research · 2017Article
- Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation.Annual review of analytical chemistry (Palo Alto, Calif.) · 2016Review
- Discovering and understanding oncogenic gene fusions through data intensive computational approaches.Nucleic acids research · 2016Review
- Recurrent chimeric fusion RNAs in non-cancer tissues and cells.Nucleic acids research · 2016Article
- Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data.Nucleic acids research · 2016Article
- NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision.Nucleic acids research · 2016Article
- ccmGDB: a database for cancer cell metabolism genes.Nucleic acids research · 2016Article
- InFusion: Advancing Discovery of Fusion Genes and Chimeric Transcripts from Deep RNA-Sequencing Data.PloS one · 2016Article
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5 authors.
Funding
Abstract
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 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. Chimeras from eight organisms have been collated including novel sense-antisense (SAS) chimeras resulting from the slippage of the sense and anti-sense intragenic regions. 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. User interface allows for rapid and easy analysis of evolutionary conservation of fusions, literature references and experimental data supporting fusions in different organisms. More than 1428 cancer breakpoints have been automatically collected from public databases and manually verified to identify their correct cross-references, genomic sequences and 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.
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