ChimerDB

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ChimerDB

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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chimerdb

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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Other names: chimerdb

ChimerDB is a database of fusion sequences encompassing bioinformatics analysis of mRNA and EST sequences in the GenBank, manual collection of literature data and integration with other well known databases. Fusion transcripts with nonoverlapping alignments at multiple genomic loci were identified and filtered to remove cloning artifacts in cDNA library preparation. Fusion transcripts are classified into two groups - genuine chromosome translocation and fusion between neighboring genes owing to intergenic splicing. Literature data from pubmed abstracts and the fusion data from public resources (OMIM, Sanger CGP, Atlas chromosomes in cancer, and the Mitelman's breakpoint) are integrated to enhance the coverage and reliability. Currently, ChimerDB contains 1,258 fusion cases that involve 1,777 genes, 381 mRNA and 654 EST sequences. It can be accessed at http://genome.ewha.ac.kr/ChimerDB/.

Webpage:

Publications:

Publications

More detailed information about this field from each metasource. ×

ChimerDB 2.0--a knowledgebase for fusion genes updated
PMID: 19906715

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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ChimerDB--a knowledgebase for fusion sequences
PMID: 16381848

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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ChimerDB 4.0: an updated and expanded database of fusion genes
PMID: 31680157

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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• ChimerDB 2.0--a knowledgebase for fusion genes updated PubMed citations: 48.

  48 articles citing: ChimerDB 2.0--a knowledgebase for fusion genes updated

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  LncRNAs and PRC2: Coupled Partners in Embryonic Stem Cells. PMID:34968226

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  3D genome alterations associated with dysregulated HOXA13 expression in high-risk T-lineage acute lymphoblastic leukemia. PMID:34140506

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  Circulating Cell-Free DNA Combined to Magnetic Resonance Imaging for Early Detection of HCC in Patients with Liver Cirrhosis. PMID:33572923

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  Targeted next-generation sequencing identifies the disruption of the SHANK3 and RYR2 genes in a patient carrying a de novo t(1;22)(q43;q13.3) associated with signs of Phelan-McDermid syndrome. PMID:32536973

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  The Search for Molecular Markers in a Gene-Orphan Case Study of a Pediatric Spinal Cord Pilocytic Astrocytoma. PMID:32108034

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  Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. PMID:31639029

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  FusionScan: accurate prediction of fusion genes from RNA-Seq data. PMID:31610622

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  Circulating DNA as prognostic biomarker in patients with advanced hepatocellular carcinoma: a translational exploratory study from the SORAMIC trial. PMID:31570105

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  Comment on "A comprehensive overview and evaluation of circular RNA detection tools". PMID:31150384

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  Regional perturbation of gene transcription is associated with intrachromosomal rearrangements and gene fusion transcripts in high grade ovarian cancer. PMID:30837567

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  NCLcomparator: systematically post-screening non-co-linear transcripts (circular, trans-spliced, or fusion RNAs) identified from various detectors. PMID:30606103

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  De novo unbalanced translocations have a complex history/aetiology. PMID:30276538

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  PITDB: a database of translated genomic elements. PMID:30053269

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  Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells. PMID:29385530

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  The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. PMID:28053160

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  Kinase impact assessment in the landscape of fusion genes that retain kinase domains: a pan-cancer study. PMID:28013235

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  ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions. PMID:27899596

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  ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining. PMID:27899563

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  RWCFusion: identifying phenotype-specific cancer driver gene fusions based on fusion pair random walk scoring method. PMID:27506935

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  CoReCG: a comprehensive database of genes associated with colon-rectal cancer. PMID:27114494

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  Discovering and understanding oncogenic gene fusions through data intensive computational approaches. PMID:27105842

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  Evolutionary Insights into RNA trans-Splicing in Vertebrates. PMID:26966239

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  Exon-centric regulation of ATM expression is population-dependent and amenable to antisense modification by pseudoexon targeting. PMID:26732650

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  Proteogenomics from a bioinformatics angle: A growing field. PMID:26670565

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  NCLscan: accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. PMID:26442529

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  Transcriptome Profiling of Pediatric Core Binding Factor AML. PMID:26397705

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  FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events. PMID:26384373

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  Biogenesis, identification, and function of exonic circular RNAs. PMID:26230526

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  An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples. PMID:26132974

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  Recurrent BCAM-AKT2 fusion gene leads to a constitutively activated AKT2 fusion kinase in high-grade serous ovarian carcinoma. PMID:25733895

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  The landscape and therapeutic relevance of cancer-associated transcript fusions. PMID:25500544

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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. PMID:25414346

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  Onco-proteogenomics: cancer proteomics joins forces with genomics. PMID:25357240

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  Transcription-mediated chimeric RNAs in prostate cancer: time to revisit old hypothesis? PMID:25188740

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  Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer. PMID:25183062

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  Is an observed non-co-linear RNA product spliced in trans, in cis or just in vitro? PMID:25053845

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  Identification of gene fusions from human lung cancer mass spectrometry data. PMID:24564548

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  CNVannotator: a comprehensive annotation server for copy number variation in the human genome. PMID:24244640

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  Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency. PMID:24131564

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  Web-based visual analysis for high-throughput genomics. PMID:23758618

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  FUSIM: a software tool for simulating fusion transcripts. PMID:23323884

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  ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. PMID:23143107

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  Gene Fusion Markup Language: a prototype for exchanging gene fusion data. PMID:23072312

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  Novel domain combinations in proteins encoded by chimeric transcripts. PMID:22689780

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  Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. PMID:22588898

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  Spatial proximity and similarity of the epigenetic state of genome domains. PMID:22496774

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  R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data. PMID:22287631

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  dbCRID: a database of chromosomal rearrangements in human diseases. PMID:21051346
• ChimerDB--a knowledgebase for fusion sequences PubMed citations: 22.

  22 articles citing: ChimerDB--a knowledgebase for fusion sequences

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  AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana. PMID:30624648

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  Discovery of New Fusion Transcripts in a Cohort of Pediatric Solid Cancers at Relapse and Relevance for Personalized Medicine. PMID:30509566

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  Conserved Gene Microsynteny Unveils Functional Interaction Between Protein Disulfide Isomerase and Rho Guanine-Dissociation Inhibitor Families. PMID:29222525

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  Trans-activation of small EDRK-rich factor 2 (SERF2) promoter by Heat Shock Factor 1. PMID:28955905

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  ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions. PMID:27899596

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  ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining. PMID:27899563

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  Discovering and understanding oncogenic gene fusions through data intensive computational approaches. PMID:27105842

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  FusionCancer: a database of cancer fusion genes derived from RNA-seq data. PMID:26215638

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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. PMID:25414346

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  ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. PMID:23143107

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  Alternative 3'-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. PMID:22960638

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  Identification and analysis of pig chimeric mRNAs using RNA sequencing data. PMID:22925561

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  Novel domain combinations in proteins encoded by chimeric transcripts. PMID:22689780

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  Novel mechanism of conjoined gene formation in the human genome. PMID:22231539

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  Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. PMID:20967262

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  Second generation sequencing of the mesothelioma tumor genome. PMID:20485525

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  ChimerDB 2.0--a knowledgebase for fusion genes updated. PMID:19906715

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  A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. PMID:19379481

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  Evaluation of paired-end sequencing strategies for detection of genome rearrangements in cancer. PMID:18404202

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  HYBRIDdb: a database of hybrid genes in the human genome. PMID:17519042

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  Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data. PMID:17330142

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  The regulated expression of chimeric tyrosine hydroxylase-insulin transcripts during early development. PMID:16840532
• ChimerDB 4.0: an updated and expanded database of fusion genes PubMed citations: 13.

  13 articles citing: ChimerDB 4.0: an updated and expanded database of fusion genes

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  Identification of human gene research articles with wrongly identified nucleotide sequences. PMID:35022248

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  FusionGDB 2.0: fusion gene annotation updates aided by deep learning. PMID:34755868

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  Clinical application of whole transcriptome sequencing for the classification of patients with acute lymphoblastic leukemia. PMID:34340673

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  Fusion gene map of acute leukemia revealed by transcriptome sequencing of a consecutive cohort of 1000 cases in a single center. PMID:34135310

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  Algorithm-Based Meta-Analysis Reveals the Mechanistic Interaction of the Tumor Suppressor LIMD1 With Non-Small-Cell Lung Carcinoma. PMID:33869018

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  CRTC1/MAML2 directs a PGC-1α-IGF-1 circuit that confers vulnerability to PPARγ inhibition. PMID:33626346

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  Emerging oncogenic fusions other than ALK, ROS1, RET, and NTRK in NSCLC and the role of fusions as resistance mechanisms to targeted therapy. PMID:33489822

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  Identification of a Novel CSNK2A1-PDGFRB Fusion Gene in a Patient with Myeloid Neoplasm with Eosinophilia. PMID:33421986

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  The landscape of long noncoding RNA-involved and tumor-specific fusions across various cancers. PMID:33275145

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  Mining potentially actionable kinase gene fusions in cancer cell lines with the KuNG FU database. PMID:33257674

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  Whole transcriptome sequencing detects a large number of novel fusion transcripts in patients with AML and MDS. PMID:33147338

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  Bioinformatics services for analyzing massive genomic datasets. PMID:32224841

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  The landscape of chimeric RNAs in non-diseased tissues and cells. PMID:31965184

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Tags

More detailed information about this field from each metasource. ×

nucleotide sequence databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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gene structure, introns and exons, splice sites

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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human genes and diseases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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cancer gene databases

metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

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gene transcripts

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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gene structure

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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gene expression

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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dna

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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sequencing

metasource: bio.tools
version: extracted_at: 2022-11-04T11:29:40.422934

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nucleic acid sequence gene structure, introns and exons, splice sites human genes and diseases cancer-related genes gene transcripts gene structure gene expression dna sequencing