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COSMIC / Catalogue Of Somatic Mutations In Cancer
Enables to explore the impact of somatic mutations in human cancer. COSMIC is a database system that collects these somatic mutation data from a variety of public sources into one standardized repository, and make it easily explorable in a variety of graphical, tabulated and downloadable ways. The database encompasses all forms of human cancer. COSMIC is built primarily via curation of published literature by expert scientists. The database is also available for download in multiple formats.
Mitelman Database / Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer
Relates chromosomal aberrations to tumor characteristics, based either on individual cases or associations. Mitelman Database provides data manually chosen from the literature. It contains more than 68 000 cases and over 11 000 gene fusions. This database in sub-divided into three parts supplying: data that relates chromosomal aberrations to specific tumor characteristics in individual patient cases; molecular biology and clinical associations; and references.
Offers fusion genes encompassing analysis of deep sequencing data and manual curations. ChimerDB is composed of three modules: ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. RNA-Seq data of The Cancer Genome Atlas (TCGA) project covering 4569 patients in 23 cancer types were analysed using two reliable programs of FusionScan and TopHat-Fusion. The user interface supports diverse search options and graphic representation of fusion gene structure.
Offers chimeric transcripts and RNA-seq matched with protein-protein interactions. ChiTaRS database 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 34922 chimeric transcripts along with 11714 cancer breakpoints, from eight organisms, and includes the manual annotation of 200 sense-antiSense (SaS) chimeras. Multiple cross-references to GeneCards, iHop, PubMed, NCBI, Ensembl, OMIM, RefSeq and the Mitelman collection are included for every entry in the ‘Full Collection’. For every chimera, a predicted chimeric protein-protein interaction (ChiPPI) network has been added. It allows for easy visualization of protein partners of both parental and fusion proteins for all human chimeras.
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A database which provides detailed information regarding the exploration of a specific hybrid gene of interest. HYBRIDdb encompasses the bioinformatics analysis of mRNA, EST, cDNA and can be used to identify hybrid transcripts created by chromosomal-mediated translocation and intergenic splicing-mediated gene fusion. The HYBRIDdb database provide genome scientists with insight into potential roles for hybrid genes in human evolution and disease.
dbCRID / database of Chromosomal Rearrangements In Diseases
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Documents the type of the event, the disease or symptoms associated, and detailed information about the chromosomal rearrangement (CR) event including precise breakpoint positions, junction sequences, genes and gene regions disrupted and experimental techniques applied to discover - analyze the CR event. Compared to these resources, dbCRID is the only database that (i) documents CR events associated with both tumor and non-tumor diseases, (ii) covers all seven types of CR events, (iii) provides break-point position information in three different precision levels, (iv) provides detailed junction sequence information, (v) documents experimental methods applied in original studies, (vi) provides detailed information about disrupted genes and gene regions and (vii) provides an intuitive browser view for examining the CR events.
Constitutes a resource dedicated to in-depth analysis of bacterial and archaeal gene fusion events. FusionDB reduces the number of false positives, at the expense of a potentially similarly high number of false negatives. To recover from this drawback, gene fusion events between genes from different genomes that belong to the same cluster of orthologous groups (COG). The extension to COG fusion events also provides information on general gene fusion tendencies in a whole bacterial genomic context. FusionDB may be searched by gene name, gene annotation, gene function, COG identifier or simply by entering an amino acid sequence. Output in full-page mode contains visualization of the different alignments that were used for scoring, and in the case of gene pairs that both belong to a COG a special COG-analysis page is provided.
A database of functional and regulatory elements of cancer-associated fusion events. FARE-CAFE is a database with the combination of the cancer related chromosomal translation events, fusion genes, domains, domain-domain interactions (DDI), protein-protein interactions (PPI), transcription factors(TF) and miRNAs collectively with the consequent experimental information. The significance of this database is currently, there is no database endow with fusion proteins role in terms of PPI and DDI in oncogenesis. This database provides detailed information about cancer related fusion genes regulatory (TFs and their target miRNA) and functional elements (domains, DDIs, PPIs). FARE-CAFE database will helpful to demonstrate clear understanding on molecular mechanism of cancer progression and ultimately pilot to the expansion of novel therapeutic approaches.
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