A chromosomal rearrangement (CR) event occurs as a consequence of double-strand breaks (DSBs) of the DNA, followed by abnormal rejoining of the non-homologous ends, producing a new chromosomal arrangement. Alternatively, a CR event can result from crossing-over between repetitive DNA sequences. CR events may lead to disruption of genes and other functional structures. They have been implicated in many tumor and non-tumor human diseases, and are frequently examined in clinical diagnosis, treatment and prognosis.
Offers an online catalog of human genes and genetic disorders. OMIM is a database human genes and genetic disorders and traits. It focuses on the molecular relationship between genetic variation and phenotypic expression. Moreover, it is based on the published peer-reviewed biomedical literature and is used by overlapping and diverse communities of clinicians, molecular biologists and genome scientists.
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.
An accessible online repository of genetic variation with associated phenotypes that facilitates the identification and interpretation of pathogenic genetic variation in patients with rare disorders. Contributing to DECIPHER is an international consortium of >200 academic clinical centres of genetic medicine and ≥1600 clinical geneticists and diagnostic laboratory scientists. Information integrated from a variety of bioinformatics resources, coupled with visualization tools, provides a comprehensive set of tools to identify other patients with similar genotype-phenotype characteristics and highlights potentially pathogenic genes.
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.
A browsable repository of personalized cancer DNA breakpoint profiles mapped over the entire genomes of 99 cancer and matched control pairs from five cancer types viz. glioblastoma multiforme (GBM), breast invasive carcinoma (BRC), lung adenocarcinoma (LUAD), ovarian serous cystadenocarcinoma (OV) and head and neck squamous cell carcinoma (HN). We also provide functionality of visualizing and comparing DNA breakpoint profiles between samples of same cancer type or across different cancer types using BreCAN-DB. Users can download breakpoint profiles from the database or may submit their data to be integrated in BreCAN-DB.
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.
A manually curated database containing a unified description of all published chromothripsis cases and relevant genomic aberrations. Currently, 423 chromothripsis samples representing 107 research articles are included in our database. The data-browsing interface allows researchers to browse the database by studies. Clicking on the article title leads to a page that includes a table with detailed information of the study and a visualization of chromothripsis cases. ChromothripsisDB represents an extraordinary resource for mining the existing knowledge of chromothripsis, and will facilitate the identification of mechanisms involved in this phenomenon.
An online database system of cross-referenced information and resources on Brassicaceae taxonomy, systematics, evolution, traits and germplasm resources. Biological material and resources, either collected directly in the wild or held in germplasm collections, are often taxonomically misidentified and are very rarely further characterized and documented. BrassiBase will close these various gaps and provide the full potential of research focusing on the adaptive characters and character trait evolution in the Brassicaceae.
Collects and provides detailed, curated clinical and molecular information on rare unbalanced chromosome aberrations. ECARUCA is an online database that aims to store only genomic imbalances that are considered to be causative for the patient’s clinical phenotype. Moreover, this repository contains data from over 4800 patients with a total of more than 6600 aberrations of which 2500 are unique chromosome aberrations.
A database that describes the genomic location of 1,374 translocation breakpoints in human tumors, corresponding to 431 different genes. TICdb is highly curated and all breakpoints are located to specific introns or exons of Ensembl transcripts, many of them at a nucleotide-scale level of resolution. For every fusion, TICdb will return the HGNC name of both partner genes and the original reference, as well as the fusion sequence.
Provides a public platform for investigators to share and compare their molecular cytogenetic data. SKY/M-FISH & CGH Database is open to everyone and all users can view an individual investigator's public data or compare public cases from different investigators. Those wishing to contribute their own data must register and can choose to keep their data private for a period not to exceed two years.
Gathers a set of human chromosomal fragile sites (CFS) and associated data related to gene-disease relationship and miRNA. HumCFS is composed of a manually curated list of about 120 experimentally verified molecularly cloned human chromosomal fragile sites for the entire somatic chromosome except for the sex chromosomes X and Y. This database can serve to conduct searches about gene related to functional categories of a disease known as moonlight property.
A database for identifying cytogenetic abnormalities. CytoD contains 17,510 abstracts from PubMed. These abstracts are determined to be related to cytogenetics because they contain standard cytogenetic abnormality terms. CytoD also allows users to search for publications using standard cytogenetics nomenclature.
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 comprehensive fusion gene database derived only from cancer RNA-seq data. FusionCancer provides a user-friendly utility for the cancer research community. A flexible query engine has been developed for the acquisition of annotated information of cancer fusion genes, which would help users to determine the chimera events leading to functional changes.