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http://ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019.BGMUT was database that provided publicly accessible platform for DNA sequences and curated set of blood mutation information. Data Archive are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive.

Proper citation: Blood Group Antigen Gene Mutation Database (RRID:SCR_002297) Copy   

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http://scicrunch.org

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2019.

Database for those interested in the consequences of Factor VIII genetic variation at the DNA and protein level, it provides access to data on the molecular pathology of haemophilia A. The database presents a review of the structure and function of factor VIII and the molecular genetics of haemophilia A, a real time update of the biostatistics of each parameter in the database, a molecular model of the A1, A2 and A3 domains of the factor VIII protein (based on the crystal structure of caeruloplasmin) and a bulletin board for discussion of issues in the molecular biology of factor VIII. The database is completely updated with easy submission of point mutations, deletions and insertions via e-mail of custom-designed forms. A methods section devoted to mutation detection is available, highlighting issues such as choice of technique and PCR primer sequences. The FVIII structure section now includes a download of a FVIII A domain homology model in Protein Data Bank format and a multiple alignment of the FVIII amino-acid sequences from four species (human, murine, porcine and canine) in addition to the virtual reality simulations, secondary structural data and FVIII animation already available. Finally, to aid navigation across this site, a clickable roadmap of the main features provides easy access to the page desired. Their intention is that continued development and updating of the site shall provide workers in the fields of molecular and structural biology with a one-stop resource site to facilitate FVIII research and education. To submit your mutants to the Haemophilia A Mutation Database email the details. (Refer to Submission Guidelines)

Proper citation: HAMSTeRS - The Haemophilia A Mutation Structure Test and Resource Site (RRID:SCR_006883) Copy   

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https://www.ddbj.nig.ac.jp/jga/index-e.html

A service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted. The JGA accepts only de-identified data approved by JST-NBDC. The JGA implements access-granting policy whereby the decisions of who will be granted access to the data resides with the JST-NBDC. After data submission the JGA team will process the data into databases and archive the original data files. The accepted data types include manufacturer-specific raw data formats from the array-based and new sequencing platforms. The processed data such as the genotype and structural variants or any summary level statistical analyses from the original study authors are stored in databases. The JGA also accepts and distributes any phenotype data associated with the samples. For other human biological data, please contact the NBDC human data ethical committee.

Proper citation: Japanese Genotype-phenotype Archive (JGA) (RRID:SCR_003118) Copy   

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http://www.genome.jp/kegg/expression/

Database for mapping gene expression profiles to pathways and genomes. Repository of microarray gene expression profile data for Synechocystis PCC6803 (syn), Bacillus subtilis (bsu), Escherichia coli W3110 (ecj), Anabaena PCC7120 (ana), and other species contributed by the Japanese research community.

Proper citation: Kyoto Encyclopedia of Genes and Genomes Expression Database (RRID:SCR_001120) Copy   

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http://www.morpholinodatabase.org/

Central database to house data on morpholino screens currently containing over 700 morpholinos including control and multiple morpholinos against the same target. A publicly accessible sequence-based search opens this database for morpholinos against a particular target for the zebrafish community. Morpholino Screens: They set out to identify all cotranslationally translocated genes in the zebrafish genome (Secretome/CTT-ome). Morpholinos were designed against putative secreted/CTT targets and injected into 1-4 cell stage zebrafish embryos. The embryos were observed over a 5 day period for defects in several different systems. The first screen examined 184 gene targets of which 26 demonstrated defects of interest (Pickart et al. 2006). A collaboration with the Verfaillie laboratory examined the knockdown of targets identified in a comparative microarray analysis of hematopoietic stem cells demonstrating how microarray and morpholino technologies can be used in conjunction to enrich for defects in specific developmental processes. Currently, many collaborations are underway to identify genes involved in morphological, kidney, skin, eye, pigment, vascular and hematopoietic development, lipid metabolism and more. The screen types referred to in the search functions are the specific areas of development that were examined during the various screens, which include behavior, general morphology, pigmentation, toxicity, Pax2 expression, and development of the craniofacial structures, eyes, kidneys, pituitary, and skin. Only data pertaining to specific tests performed are presented. Due to the complexity of this international collaboration and time constraints, not all morpholinos were subjected to all screen types. They are currently expanding public access to the database. In the future we will provide: * Mortality curves and dose range for each morpholino * Preliminary data regarding the effectiveness of each morpholino * Expanded annotation for each morpholino * External linkage of our morpholino sequences to ZFIN and Ensembl. To submit morpholino-knockdown results to MODB please contact the administrator for a user name and password.

Proper citation: Morpholino Database (RRID:SCR_001378) Copy   

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http://www.ncbi.nlm.nih.gov/gtr/

Central location for voluntary submission of genetic test information by providers including the test''s purpose, methodology, validity, evidence of the test''s usefulness, and laboratory contacts and credentials. GTR aims to advance the public health and research into the genetic basis of health and disease. GTR is accepting registration of clinical tests for Mendelian disorders, complex tests and arrays, and pharmacogenetic tests. These tests may include multiple methods and may include multiple major method categories such as biochemical, cytogenetic, and molecular tests. GTR is not currently accepting registration of tests for somatic disorders, research tests or direct-to-consumer tests.

Proper citation: Genetic Testing Registry (RRID:SCR_005565) Copy   

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https://www.ebi.ac.uk/eva/

Open access database of all types of genetic variation data from all species. Users can download data from any study, or submit their own data to archive. You can also query all variants by study, gene, chromosomal location or dbSNP identifier using our Variant Browser.

Proper citation: European Variation Archive (EVA) (RRID:SCR_017425) Copy   

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http://www.plexdb.org/index.php

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data. The integrated tools of PLEXdb allow investigators to use commonalities in plant biology for a comparative approach to functional genomics through use of large-scale expression profiling data sets.

Proper citation: PLEXdb - Plant Expression Database (RRID:SCR_006963) Copy   

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http://rgd.mcw.edu

Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources.

Proper citation: Rat Genome Database (RGD) (RRID:SCR_006444) Copy   

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http://locus.jouy.inra.fr/cgi-bin/bovmap/intro.pl

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing.

Proper citation: BovMap Database (RRID:SCR_008145) Copy   

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http://www.arabidopsis.org

Database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from data pages to other Arabidopsis resources. The data can be searched, viewed and analyzed. Datasets can also be downloaded. Pages on news, job postings, conference announcements, Arabidopsis lab protocols, and useful links are provided.

Proper citation: TAIR (RRID:SCR_004618) Copy   

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http://www.ncbi.nlm.nih.gov/SNP/

Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource.

Proper citation: dbSNP (RRID:SCR_002338) Copy   

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http://www.humgen.rwth-aachen.de/

Catalog of all changes detected in PKHD1 (Polycystic Kidney and Hepatic Disease 1) in a locus specific database. Investigators are invited to submit their novel data to this database. These data should be meaningful for clinical practice as well as of relevance for the reader interested in molecular aspects of polycystic kidney disease (PKD). There are also some links and information for ARPKD patients and their parents. Autosomal recessive polycystic kidney disease (ARPKD/PKHD1) is an important cause of renal-related and liver-related morbidity and mortality in childhood. This study reports mutation screening in 90 ARPKD patients and identifies mutations in 110 alleles making up a detection rate of 61%. Thirty-four of the detected mutations have not been reported previously. Two underlying mutations in 40 patients and one mutation in 30 cases are disclosed, and no mutation was detected on the remaining chromosomes. Mutations were found to be scattered throughout the gene without evidence of clustering at specific sites. PKHD1 mutation analysis is a powerful tool to establish the molecular cause of ARPKD in a given family. Direct identification of mutations allows an unequivocal diagnosis and accurate genetic counseling even in families displaying diagnostic challenges.

Proper citation: Autosomal Recessive Polycystic Kidney Disease Mutation Database (RRID:SCR_002290) Copy   

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http://www.genet.sickkids.on.ca/cftr/

Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.

Proper citation: Cystic Fibrosis Mutation Database (RRID:SCR_000685) Copy   

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http://www.type2diabetesgenetics.org/

Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease.

Proper citation: Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) Copy   

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