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TCGA Data Portal / The Cancer Genome Atlas Data Portal
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Generates, analyzes, and makes available genomic sequence, expression, methylation, and copy number variation (CNV) data on over 11,000 individuals who represent over 30 different types of cancer. The information generated by TCGA is centrally managed and entered into databases as it becomes available, making the data rapidly accessible to the entire research community. TCGA is a collaborative effort led by the National Cancer Institute and the National Human Genome Research Institute to map the genomic and epigenomic changes that occur in types of human cancer, including nine rare tumors. Its goal is to support new discoveries through the generation of a catalog of somatic aberrations occurring in the different neoplasms, and accelerate the pace of research aimed at improving the diagnosis, treatment, and prevention of cancer.
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.
HGMD / Human Gene Mutation Database
Compiles information related to disease-related functional genetic variation in the germline. HGMD includes more than 200000 mutation entries, manually curated, obtained from the scientific literature. The database can be consulted in two formats: a public and a commercial version providing additional features. It can be used for supporting the pathological authenticity and/or novelty of detected gene lesions, establishing an overview of the mutational spectra for specific genes.
VarSome
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A knowledge base and aggregator for human genomic variants. VarSome gives fast access to more than 33 billion items of variant and gene annotation sourced from public databases. It also provides advanced visualisations and features such as functinal annotation for any variant, known or unknown, as well as automated variant classification based on professional guidelines. Its tens of thousands of users add an fast-growing amount of their own insights on its pages. Users may also deploy the associated API to obtain data directly into their software.
SEECancer / Somatic Events in Evolution of Cancer genome
Provides a comprehensive resource of cancer evolutionary stage-specific events and their temporal orders. SEECancer is an online database containing over 1200 cancer evolutionary stage-specific somatic events. It supplies several features for browsing the query results: (1) users can filter entries by typing any term in the ‘Search’ field on the top right side above the table; (2) they can sort columns in an ascending fashion; (3) the table size per page can be selected by using the ‘Show entries’ pull-down menu.
mSignatureDB
Compiles information about mutational signatures in 73 TCGA/ICGC cancer projects. mSignatureDB is composed of four main panels: (i) the browse panel allows users to manipulate landscapes and contributions of mutational signatures according multiple views; (ii) the search panel authorizes to explore TCGA/ICGC cancer projects, individual sample or run cross-project comparisons; (iii) the analysis panel provides an interface for deconstructSigs and R-based WTSI Mutational Signature Framework software and; (iv) the download panel permits loading of mutational signature patterns of TCGA/ICGC tumors.
BreCAN-DB / BREakpoint profiles of CANcer genomes DataBase
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.
CTD2 Data Portal / Cancer Target Discovery And Development Data Portal
Compiles network-generated summaries about key cancer biology findings and cancer-relevant results related to proteins, genes and compounds. The Cancer Target Discovery and Development Data Portal is an open-access data portal that serves as the single access point for downloading CTD2 data. This resource mines and validates data from large-scale adult and pediatric cancer genome characterization initiatives and advances them toward use in precision oncology.
CGTD / Cancer Gene Trust Daemon
An online network for sharing somatic cancer genomic and clinical data from around the world, making the data accessible for research use in real time. CGTD provides a basic HTML interface and RESTful API to add, list and authenticate submissions as well as the peering relationship between stewards. Submissions consist of a JSON manifest with a list of fields and files. Fields typically include de-identified clinical data (i.e. tumor type). Files typically consist of somatic variant vcf files and gene expression tsv file. Manifest's and files are stored and referenced by the multihash of their content.
Genome Trax
A comprehensive compilation of variant knowledge that is made available for download for easy integration into your own custom variant analysis pipeline for human whole genome, exome and targeted sequences. With Genome Trax™ content you can confidently identify known pathogenic variants or explore novel, as-yet-uncharacterized variants found within your sequence samples that are predicted to have a deleterious effect by virtue of a change in amino acid, disruption of a regulatory motif, or the disease-, drug-, or pathway-association of the affected gene. The database includes the world’s most comprehensive collection of inherited disease causing mutations from HGMD® Professional and pharmacogenomic variants from PGMD™, as well as regulatory sites from TRANSFAC®, and disease genes, drug targets and pathways from PROTEOME™. It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations.
CancerGD / Cancer Genetic Dependencies Database
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Integrates genotypic profiling with largescale loss-of-function genetic screens in tumor cell lines to identify such genetic dependencies. CancerGD provides tools for searching, visualizing, and interpreting these cancer genetic dependencies (CGD) through the integration of functional interaction networks. 36 associated driver genes were selected based on their identification in multiple independent analyses and due to their alteration in at least five tumor cell lines featured in one or more of the included loss-of-function screens. Driver gene associated CGDs are identified both across cell lines from multiple histologies (‘Pan Cancer’) and within tumor cell lines arising from specific primary sites (e.g. ‘Breast’).
HCAD / Human Chromosome Aberration Database
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Gathers textual and comprehensive information of registered genes. HCAD supplies over 700 breakpoints and integrates literature associations to about 800 genes from 2000 cytogenetically different translocations and inversions. Besides, the database provides statistical analysis which allows to determine if genes can be relevant for a certain breakpoint. False positive associations of these predicted genes are eliminated by crosschecking their localization with genomic data.
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