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http://rulai.cshl.edu/tred

Collects mammalian cis- and trans-regulatory elements together with experimental evidence. Regulatory elements were mapped on to assembled genomes. Resource for gene regulation and function studies. Users can retrieve primers, search TF target genes, retrieve TF motifs, search Gene Regulatory Networks and orthologs, and make use of sequence analysis tools. Uses databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. Manually curated.

Proper citation: Transcriptional Regulatory Element Database (RRID:SCR_005661) Copy   

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http://snpselector.duhs.duke.edu/hqsnp36.html

This is the HQSNP DB (high-quality SNP database) developed by CHG bioinformatics group. The high-quality SNP is defined as a SNP having allele frequency or genotyping data. The majority of the HQSNPs come from HapMap, others come from JSNP (Japanese SNP database), TSC (The SNP Consortium), Affymetrix 120K SNP, and Perlegen SNP. There are four kinds of SNP search you can do: * Get SNPs by dbSNP rs#: Choose this search if you have already selected a list of SNPs and you just want to get the SNP information. The program will generate a Excel file containing the SNP flanking sequence, variation, quality, function, etc. In the Excel file, there are 10 highlighted fields. You can send only those highlighted information to Illumina to get SNP pre-score. (The same fields are presented in other types of searches as well.) * Get gene SNPs by gene names: Choose this search if you have a list of gene names and you want to get the SNP information in these genes. The gene name can be official gene symbol, Ensembl gene ID, RefSeq accession ID, LocusLink number, etc. * Get gene SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get all gene SNP information in these regions. The software will find all the Ensembl genes in the regions and find SNPs associated to each Ensembl gene. * Get genome scan SNPs by genome regions: Choose this search if you have a list of genome regions and you want to get evenly spaced SNPs in these regions. A SNP selection tool (SNPselector) was built upon HQSNP. It took snp ID list, gene name list, or genome region list as input and searched SNPs for genome scan or gene assoctiation study. It could take an optional ABI SNP file (exported from ABI SNP search web page) as input for checking whether the candidate SNP is available from ABI. It could also take an optional Illumina SNP pre-score file as input to select SNP for Illumina SNP assay. It generated results sorted by tag SNP in LD block, SNP quality, SNP function, SNP regulatory potential, and SNP mutation risk. SNPselector is now retired from public use (as of September 30, 2010).

Proper citation: High Quality SNP Database (RRID:SCR_007230) Copy   

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http://cmckb.cellmigration.org

It is a database of keys facts about proteins, families, and complexes involved in cell migration. This ongoing project provides a large amount of automated and curated data, collected from numerous online resources that are updated monthly. These data include names, synonyms, sequence information, summaries, CMC research data, reagents, structures, as well as protein family and complex details. CMKB''s ultimate goal is to create a database that will enable the cell migration community to conveniently access significant information about molecules of interest. This will also serve as a stepping stone to pathway analysis and demonstrate how these molecules coordinate with one another during cell adhesion and movement. Sponsors: This resource is supported by the Cell Migration Consortium.

Proper citation: CMKB (RRID:SCR_007229) Copy   

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http://www.oreganno.org/oregano/

Open source, open access database and literature curation system for community based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. Automatically cross referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, eVOC: Cell type ontology, and Taxonomy database. Community driven resource for curated regulatory annotation.

Proper citation: Open Regulatory Annotation Database (RRID:SCR_007835) Copy   

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https://leger2.helmholtz-hzi.de/cgi-bin/expLeger.pl

Knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species.Provides information on gene functions (as annotated or supposed by literature from homologous organisms) , protein expression levels under defined experimental conditions ,subcellular localization of proteins (expected and/or experimentally validated) , biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology.

Proper citation: LEGER: the post-genome Database for Listeria Research (RRID:SCR_007760) Copy   

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http://www.genepath.org/

GenePath is a web-enabled intelligent assistant for the analysis of genetic data and for discovery of genetic networks. GenePath uses abductive inference to elucidate network constraints and logic to derive consistent networks. Typically, it starts with a set of genetic experiments, uses a set of embedded rules (patterns) to infer relations between genes and outcome, and based on these relations constructs a genetic network.

Proper citation: GenePath (RRID:SCR_007974) Copy   

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http://genomics.senescence.info/genes/

Collection of annotated and manually curated data of genes related to aging divided into genes related to longevity and/or aging in model organisms (yeast, worms, flies, mice, etc.) and aging related human genes.

Proper citation: GenAge (RRID:SCR_010223) Copy   

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http://www.alzforum.org/res/com/ant/

The Alzheimer Research Forum is the web''s most dynamic scientific community dedicated to understanding Alzheimer''s disease and related disorders. It also contains a database of providers of antibodies directed against several hundred molecules and proteins of relevant to research on Alzheimer and other neurodegenerative diseases. The web site reports on the latest scientific findings, from basic research to clinical trials; creates and maintains public databases of essential research data and reagents, and produces discussion forums to promote debate, speed the dissemination of new ideas, and break down barriers across the numerous disciplines that can contribute to the global effort to cure Alzheimer''s disease. The ARF team of professional science writers and editors, information technology experts, web developers and producers all work closely with our distinguished and diverse Advisory Board to ensure a high-quality of information and services. We very much welcome our readers'' participation in all aspects of the web site. Sponsors: The Alzheimer Research Forum is an independent nonprofit organization. It is supported by grants and individual donations.

Proper citation: Alzforum Antibody Directory for Neuroscience Research (RRID:SCR_013601) Copy   

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http://web.stanford.edu/group/barres_lab/brain_rnaseq.html

Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

Proper citation: Brain RNA-Seq (RRID:SCR_013736) Copy   

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http://thecellmap.org

Web accessible database for visualizing and mining global yeast genetic interaction network. Allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize sub networks, using data driven network layouts in intuitive and interactive manner. Used for storing and visualizing genetic interactions in S. cerevisiae.

Proper citation: TheCellMap (RRID:SCR_018728) Copy   

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https://phenodb.org/

Database for phenotype genotype associations for humans. Used by clinical researchers to store standardized phenotypic information, diagnosis, and pedigree data and then run analyses on VCF files from individuals, families or cohorts with suspected Mendelian disease.

Proper citation: PhenoDB (RRID:SCR_016551) Copy   

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https://www.sdu.dk/da/Om_SDU/Institutter_centre/Ist_sundhedstjenesteforsk/Centre/DTR.aspx?sideid=index&sprog=eng

Twin registry to studying causes of cancer, gene inheritance and environment. Contains information on twins born in Denmark. Comprises twins born through more than 125 years.

Proper citation: Danish Twin Registry (RRID:SCR_017482) Copy   

•   Source: SciCrunch Registry
  

https://divdb.jax.org/

Database provides access to genotype and phenotype data from experiments with Diversity Outbred mice. Data can be searched by publication, investigator, and data type and can be downloaded in zipped CSV or R/QTL2 formats. Users can download full studies or subset of samples, genotypes, clinical phenotypes and molecular phenotypes including transcript, proteomic, and metabolomic profiling data.

Proper citation: Diversity Outbred Database (RRID:SCR_018180) Copy   

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https://hive.biochemistry.gwu.edu/dna.cgi?cmd=tissue_codon_usage&id=586358&mode=cocoputs

Database includes genomic codon-pair and dinucleotide statistics of all organisms with sequenced genome. Facilitates genetic variation analyses and recombinant gene design. Derived from all available GenBank and RefSeq data.

Proper citation: Codon and Codon-Pair Usage Tables (RRID:SCR_018504) Copy   

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https://dbaasp.org

Collection of manually curated data regarding structure and antimicrobial activity of natural and synthetic peptides. Provides the information and analytical resources to develop antimicrobial compounds with the high therapeutic index.

Proper citation: Database of Antimicrobial Activity and Structure of Peptides (RRID:SCR_016600) Copy   

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http://p300db.choudharylab.org

Data collection of CBP/p300 regulated acetylome, proteome, and transcriptome in murine embryonic fibroblasts. Composed of Symbol search for quantified acetylation sites, proteins and transcripts abundance in CBP/p300, Domain search for batch query of proteins by specific domain and Conserved sites for acetylation sites that are conserved between mouse and human, and their regulation in KATi treated cells.

Proper citation: p300db (RRID:SCR_017063) Copy   

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https://www.sdbonline.org/sites/fly/atlas/00atlas.htm

Collection of color illustrations that follow main events of embryogenesis and post embryonic development of Drosophila.

Proper citation: Atlas of Drosophila Development (RRID:SCR_017506) Copy   

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http://www.regulomedb.org/

Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.

Proper citation: RegulomeDB (RRID:SCR_017905) Copy   

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http://cometa.tigem.it/

Interactive database of miRNA targets and miRNA-regulated gene networks to integrate expression data from hundreds of cellular and tissue conditions. Website includes CoMeTa corank lists and additional targets for all of human miRNAs, their associated pathways resulting from COOL analysis, and miRNA communities with their corresponding enriched functional categories. Website is searchable by miRNA, target gene, or biological function of interest, and represents unique resource to gain insight into miRNA-controlled gene networks and functions.

Proper citation: CoMeTa Website (RRID:SCR_017357) Copy   

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http://mirtarbase.mbc.nctu.edu.tw/

Web based manually curated experimentally validated database of microRNA-Target interactions. Collection of MTIs data validated experimentally by reporter assays, western blot, or microarray experiments with overexpression or knockdown of miRNAs.

Proper citation: miRTarBase (RRID:SCR_017355) Copy   

•   Source: SciCrunch Registry