ArticleNucleic acids research2010
ChimerDB 2.0--a knowledgebase for fusion genes updated.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Circulating DNA as prognostic biomarker in patients with advanced hepatocellular carcinoma: a translational exploratory study from the SORAMIC trial.Journal of translational medicine · 2019Trial
- De novo unbalanced translocations have a complex history/aetiology.Human genetics · 2018Trial
- Fusion-positive rhabdomyosarcoma oncofusions share a common interactome.Nature communications · 2026Article
- Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing.Nucleic acids research · 2023Article
- TargetedCell reports methods · 2023Article
- Assessing the impacts of various factors on circular RNA reliability.Life science alliance · 2023Article
- GraphChrom: A Novel Graph-Based Framework for Cancer Classification Using Chromosomal Rearrangement Endpoints.Cancers · 2022Article
- 3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia.Nature communications · 2021Article
- Circulating Cell-Free DNA Combined to Magnetic Resonance Imaging for Early Detection of HCC in Patients with Liver Cirrhosis.Cancers · 2021Article
- Targeted next-generation sequencing identifies the disruption of theMolecular cytogenetics · 2020Article
- Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods.Genome biology · 2019Article
- FusionScan: accurate prediction of fusion genes from RNA-Seq data.Genomics & informatics · 2019Article
- LncRNAs and PRC2: Coupled Partners in Embryonic Stem Cells.Epigenomes · 2019Review
- Comment on "A comprehensive overview and evaluation of circular RNA detection tools".PLoS computational biology · 2019Article
- Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer.Scientific reports · 2019Article
- NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors.BMC bioinformatics · 2019Article
- Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study.Briefings in bioinformatics · 2018Article
- Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells.Nucleic acids research · 2018Article
- PITDB: a database of translated genomic elements.Nucleic acids research · 2018Article
- Proteogenomics from a bioinformatics angle: A growing field.Mass spectrometry reviews · 2017Review
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chromosome translocations and gene fusions are frequent events in the human genome and have been found to cause diverse types of tumor. ChimerDB is a knowledgebase of fusion genes identified from bioinformatics analysis of transcript sequences in the GenBank and various other public resources such as the Sanger cancer genome project (CGP), OMIM, PubMed and the Mitelman's database. In this updated version, we significantly modified the algorithm of identifying fusion transcripts. Specifically, the new algorithm is more sensitive and has detected 2699 fusion transcripts with high confidence. Furthermore, it can identify interchromosomal translocations as well as the intrachromosomal deletions or inversions of large DNA segments. Importantly, results from the analysis of next-generation sequencing data in the short read archives are incorporated as well. We updated and integrated all contents (GenBank, Sanger CGP, OMIM, PubMed publications and the Mitelman's database), and the user-interface has been improved to support diverse types of searches and to enhance the user convenience especially in browsing PubMed articles. We also developed a new alignment viewer that should facilitate examining reliability of fusion transcripts and inferring functional significance. We expect ChimerDB 2.0, available at http://ercsb.ewha.ac.kr/fusiongene, to be a valuable tool in identifying biomarkers and drug targets.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.