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on page 1 showing 8 out of 8 results

Cite this (AnimalTFDB, RRID:SCR_001624)

URL: http://www.bioguo.org/AnimalTFDB/

Resource Type: Resource, data or information resource, database

A comprehensive transcription factor (TF) database in which they identified and classified all the genome-wide TFs in 50 sequenced animal genomes (Ensembl release version 60). In addition to TFs, it also collects transcription co-factors and chromatin remodeling factors of those genomes, which play regulatory roles in transcription. Here they defined the TFs as proteins containing a sequence-specific DNA-binding domain (DBD) and regulating target gene expression. Currently, the AnimalTFDB classifies all the animal TFs into 72 families according to their conserved DBDs. Gene lists of transcription factors, transcription co-factors and chromatin remodeling factors of each species are available for downloading.

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Cite this (DOMINE: Database of Protein Interactions, RRID:SCR_002399)

URL: http://domine.utdallas.edu

Resource Type: Resource, data or information resource, database

Database of known and predicted protein domain (domain-domain) interactions containing interactions inferred from PDB entries, and those that are predicted by 8 different computational approaches using Pfam domain definitions. DOMINE contains a total of 26,219 domain-domain interactions (among 5,410 domains) out of which 6,634 are inferred from PDB entries, and 21,620 are predicted by at least one computational approach. Of the 21,620 computational predictions, 2,989 interactions are high-confidence predictions (HCPs), 2,537 interactions are medium-confidence predictions (MCPs), and the remaining 16,094 are low-confidence predictions (LCPs). (May 2014)

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Cite this (Human Gene Mutation Database, RRID:SCR_001621)

URL: http://www.hgmd.org

Resource Type: Resource, data or information resource, database

Curated database of known (published) gene lesions responsible for human inherited disease.

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Cite this (Leiden Open Variation Database, RRID:SCR_006566)

URL: http://www.LOVD.nl/

Resource Type: Resource, data processing software, database, software application, data storage software, service resource, storage service resource, software resource, data repository, data or information resource

Freely available tool for Gene-centered collection and display of DNA variations. It also provides patient-centered data storage and storage of Next Generation Sequencing (NGS) data, even of variants outside of genes. Please note that LOVD provides a system for storage of information on genes and allelic variants. To obtain information about any genes or variants, do not download the LOVD package. This information should be obtained from the respective databases, http://www.lovd.nl/2.0/index_list.php In total: 2,507,027 variants (2,208,937 unique) in 170,935 individuals in 62619 genes in 88 LOVD installations. (Aug. 2013) LOVD 3.0 shared installation, http://databases.lovd.nl/shared/genes To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer. You can download LOVD in ZIP and GZIPped TARball formats.

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Cite this (NCBI Sequence Read Archive, RRID:SCR_004891)

URL: http://www.ncbi.nlm.nih.gov/sra

Resource Type: Resource, service resource, data or information resource, data repository, storage service resource, database

Repository of raw sequencing data from the next generation of sequencing platforms including including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, Complete Genomics, and Pacific Biosciences SMRT. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. Data submissions are welcome. SRA is NIH''''s primary archive of high-throughput sequencing data and is part of the international partnership of archives (INSDC) at the NCBI, the European Bioinformatics Institute and the DNA Database of Japan. Data submitted to any of the three organizations are shared among them. NCBI announced that due to budget constraints, it would be discontinuing SRA but NIH has since committed interim funding for SRA in its current form until October 1, 2011. In addition, NCBI has been working with staff from other NIH Institutes and NIH grantees to develop an approach to continue archiving a widely used subset of next generation sequencing data after October 1, 2011.

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    Pfam

Cite this (Pfam, RRID:SCR_004726)

URL: http://pfam.xfam.org/

Resource Type: Resource, data or information resource, database

A database of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). Users can analyze protein sequences for Pfam matches, view Pfam family annotation and alignments, see groups of related families, look at the domain organization of a protein sequence, find the domains on a PDB structure, and query Pfam by keywords. There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families that may automatically generate a supplement using the ADDA database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found. Pfam also generates higher-level groupings of related families, known as clans (collections of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM).

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    PharmGKB

Cite this (PharmGKB, RRID:SCR_002689)

URL: http://www.pharmgkb.org/

Resource Type: Resource, data access protocol, database, web service, data set, service resource, storage service resource, software resource, data repository, data or information resource

Database and central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. PharmGKB welcomes submissions of primary data from all research into genes and genetic variation and their effects on drug and disease phenotypes. PharmGKB collects, encodes, and disseminates knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways. PharmGKB is part of the NIH Pharmacogenomics Research Network (PGRN), a nationwide collaborative research consortium. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs. A selected subset of data from PharmGKB is accessible via a SOAP interface. Downloaded data is available for individual research purposes only. Drugs with pharmacogenomic information in the context of FDA-approved drug labels are cataloged and drugs with mounting pharmacogenomic evidence are listed.

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Cite this (Search Tool for Interactions of Chemicals, RRID:SCR_007947)

URL: http://stitch.embl.de

Resource Type: Resource, data or information resource, database

Database to explore known and predicted interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68,000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database.

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