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http://decipher.sanger.ac.uk/

Interactive database which incorporates a suite of tools designed to aid the interpretation of submicroscopic chromosomal imbalance. Used to enhance clinical diagnosis by retrieving information from bioinformatics resources relevant to the imbalance found in the patient. Contributing to the DECIPHER database is a Consortium, comprising an international community of academic departments of clinical genetics. Each center maintains control of its own patient data (which are password protected within the center''''s own DECIPHER project) until patient consent is given to allow anonymous genomic and phenotypic data to become freely viewable within Ensembl and other genome browsers. Once data are shared, consortium members are able to gain access to the patient report and contact each other to discuss patients of mutual interest, thus facilitating the delineation of new microdeletion and microduplication syndromes.

Proper citation: DECIPHER (RRID:SCR_006552) Copy   

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http://catmaid.org/

A toolkit designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. The interface is inspired by GoogleMaps, with which it shares basic navigation concepts, enhanced to allow the exploration of 3D biological image data acquired by optical or physical sectioning microscopy techniques. The interface enables seamless sharing of regions of interest through bookmarks and synchronized navigation through multiple registered data sets. With massive biological image data sets it is unrealistic to create a sustainable centralized repository. A unique feature of CATMAID is its partially decentralized architecture where the presented image data can reside on any Internet accessible server and yet can be easily cross-referenced in the central database. In this way no image data are duplicated and the data producers retain full control over their images. CATMAID is intended to serve as data sharing platform for biologists using high-resolution imaging techniques to probe large specimens. Any high-throughput, high-content imaging project such as gene expression pattern screens would benefit from the interface for data sharing and annotation. Features: * Fast terabyte-scale image data browsing * Collaborative microcircuit reconstruction and annotation * Flexible hierarchical semantic annotation * Multiple linked image stack display * Neuron Catalog * SVG and WebGL-based neuronal morphology viewer * Open source software

Proper citation: CATMAID (RRID:SCR_006278) Copy   

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http://biogps.org/

An extensible and customizable gene annotation portal that emphasizes community extensibility and user customizability. It is a complete resource for learning about gene and protein function. Community extensibility reflects a belief that any BioGPS user should be able to add new content to BioGPS using the simple plugin interface, completely independently of the core developer team. User customizability recognizes that not all users are interested in the same set of gene annotation data, so the gene report layouts enable each user to define the information that is most relevant to them. Currently, BioGPS supports eight species: Human (Homo sapiens), Mouse (Mus musculus), Rat (Rattus norvegicus), Fruitfly (Drosophila melanogaster), Nematode (Caenorhabditis elegans), Zebrafish (Danio rerio), Thale-cress (Arabidopsis thaliana), Frog (Xenopus tropicalis), and Pig (Sus scrofa). BioGPS presents data in an ortholog-centric format, which allows users to display mouse plugins next to human ones. Our data for defining orthologs comes from NCBI's HomoloGene database.

Proper citation: BioGPS: The Gene Portal Hub (RRID:SCR_006433) Copy   

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http://scansite.mit.edu/

Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or PDZ domains. The Motifscanner program utilizes an entropy approach that assesses the probability of a site matching the motif using the selectivity values and sums the logs of the probability values for each amino acid in the candidate sequence. The program then indicates the percentile ranking of the candidate motif in respect to all potential motifs in proteins of a protein database. When available, percentile scores of some confirmed phosphorylation sites for the kinase of interests or confirmed binding sites of the domain of interest are provided for comparison with the scores of the candidate motifs.

Proper citation: Scansite (RRID:SCR_007026) Copy   

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http://www.hprd.org

Database that represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data.

Proper citation: HPRD - Human Protein Reference Database (RRID:SCR_007027) Copy   

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http://www.biocarta.com/

BioCarta Pathways allows users to observe how genes interact in dynamic graphical models. Online maps available within this resource depict molecular relationships from areas of active research. In an open source approach, this community-fed forum constantly integrates emerging proteomic information from the scientific community. It also catalogs and summarizes important resources providing information for over 120,000 genes from multiple species. Find both classical pathways as well as current suggestions for new pathways.

Proper citation: BioCarta Pathways (RRID:SCR_006917) Copy   

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http://faostat.fao.org/

A multilingual database that provides large time-series and cross sectional data relating to hunger, food, agriculture, nutrition, fisheries, forestry and food aid by country and region from 1961 to present. Data can be searched, browsed, analyzed and downloaded.

Proper citation: FAOSTAT (RRID:SCR_006914) Copy   

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http://www.alzgene.org/

The AlzGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in Alzheimer''s disease. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data. In addition to identifying the epsilon4 allele of APOE and related effects, we pinpointed over a dozen potential Alzheimer disease susceptibility genes (ACE, CHRNB2, CST3, ESR1, GAPDHS, IDE, MTHFR, NCSTN, PRNP, PSEN1, TF, TFAM and TNF) with statistically significant allelic summary odds ratios (ranging from 1.11-1.38 for risk alleles and 0.92-0.67 for protective alleles). Our database provides a powerful tool for deciphering the genetics of Alzheimer disease, and it serves as a potential model for tracking the most viable gene candidates in other genetically complex diseases.

Proper citation: AlzGene: Field Synopsis of Genetic Association Studies in AD (RRID:SCR_006749) Copy   

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http://www.pdgene.org/

The PDGene database aims to provide a comprehensive, unbiased and regularly updated collection of genetic association studies performed on Parkinson's disease (PD) phenotypes. Eligible publications are identified following systematic searches of scientific literature databases, as well as the table of contents of journals in genetics, neurology, and psychiatry. The database can be searched either by a variety of dropdown menus or by specific keywords. For each gene, summary overviews are provided displaying key characteristics for each publication, including links to genotype distributions of the polymorphisms studied, random-effects allelic meta-analyses, and funnel plots for an assessment of publication bias. The PDGene database, developed by Massachusetts General Hospital/Harvard Medical School, The Michael J. Fox Foundation and the Alzheimer Research Forum, is supported by a grant from The Michael J. Fox Foundation in partnership with the Alzheimer Research Forum.

Proper citation: PDGene - A database for Parkinsons disease genetic association studies (RRID:SCR_006666) Copy   

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http://www.catalogueoflife.org/

Comprehensive and authoritative global index of species of animals, plants, fungi and micro-organisms. It consists of a single integrated species checklist and taxonomic hierarchy. The Catalogue holds essential information on the names, relationships and distributions of over 1.3 million species. This figure continues to rise as information is compiled from diverse sources around the world. There are two distinct versions of the Catalogue of Life: the Dynamic Checklist and the Annual Checklist. Choose the version most suited to your needs. If you have a taxonomic database and would like to join the Species 2000 federation of databases in the Catalogue of Life please contact the Species 2000 Secretariat: all candidate databases go through a peer review process. The Annual Checklist Exchange Format defines the format for exchanging data.

Proper citation: Catalogue of Life (RRID:SCR_006701) Copy   

•   Source: SciCrunch Registry

http://www.szgene.org/

The SZGene database provides a comprehensive, unbiased and regularly updated field synopsis of genetic association studies performed in schizophrenia. In addition, hundreds of up-to-date meta-analyses are available for all eligible polymorphisms with sufficient data. Eligible publications are identified following systematic searches of scientific literature databases, as well as the table of contents of journals in genetics and psychiatry. The database can be searched either by a variety of dropdown menus or by specific keywords. For each gene, summary overviews are provided displaying key characteristics for each publication, including links to genotype distributions of the polymorphisms studied, random-effects allelic meta-analyses, and funnel plots for an assessment of publication bias.

Proper citation: Schizophrenia Research Forum: Published Candidate Genes for Schizophrenia (RRID:SCR_006938) Copy   

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http://datf.cbi.pku.edu.cn/

Database that collects all arabidopsis transcription factors (totally 1922 Loci; 2290 Gene Models) and classifies them into 64 families. It uses not only locus (gene), but also gene model (transcript, protein) and the detail information is for each gene model not for locus. It adds multiple alignment of the DNA-binding domain of each family, Neighbor-Joining phylogenetic tree of each family, the GO annotation, homolog with the Database of Rice Transcription Factors (DRTF). It also keeps old information items such as the unique cloned and sequenced information of about 1200 transcription factors, protein domains, 3D structure information with BLAST hits against PDB, predicted Nuclear Location Signals, UniGene information, as well as links to literature reference.

Proper citation: Database of Arabidopsis Transcription Factors (RRID:SCR_007101) Copy   

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http://xin.cz3.nus.edu.sg/group/cjttd/ttd.asp

A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs/ligands directed at each of these targets. Also included in this database are links to relevant databases that contain information about the function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and related literatures of each target.This database currently contains 1535 targets and 2107 drugs/ligands. Queries can be submitted by entering or selecting the required information in any one or combination of the five fields in the form. User can specify full name or any part of the name in a text field, or choose one item from an selection field.

Proper citation: Therapeutic Target Database (RRID:SCR_006892) Copy   

•   Source: SciCrunch Registry

http://funspec.med.utoronto.ca/

FunSpec is a web-based tool for statistical evaluation of groups of genes and proteins (e.g. co-regulated genes, protein complexes, genetic interactors) with respect to existing annotations, including GO terms. FunSpec (an acronym for Functional Specification) inputs a list of yeast gene names, and outputs a summary of functional classes, cellular localizations, protein complexes, etc. that are enriched in the list. The classes and categories evaluated were downloaded from the MIPS Database and the GO Database . In addition, many published datasets have been compiled to evaluate enrichment against. Hypertext links to the publications are given. The p-values, calculated using the hypergeometric distribution, represent the probability that the intersection of given list with any given functional category occurs by chance. The Bonferroni-correction divides the p-value threshold, that would be deemed significant for an individual test, by the number of tests conducted and thus accounts for spurious significance due to multiple testing over the categories of a database. After the Bonferroni correction, only those categories are displayed for which the chance probability of enrichment is lower than: p-value/#CD where #CD is the number of categories in the selected database. Without the Bonferroni Correction, all categories are displayed for which the same probability of enrichment is lower than: p-value threshold in an individual test Note that many genes are contained in many categories, especially in the MIPS database (which are hierarchical) and that this can create biases for which FunSpec currently makes no compensation. Also the databases are treated as independent from one another, which is really not the case, and each is searched seperately, which may not be optimal for statistical calculations. Nonetheless, we find it useful for sifting through the results of clustering analysis, TAP pulldowns, etc. Platform: Online tool

Proper citation: FunSpec (RRID:SCR_006952) Copy   

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http://www.broadinstitute.org/mammals/haploreg/haploreg.php

HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

Proper citation: HaploReg (RRID:SCR_006796) Copy   

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http://dgv.tcag.ca/

Collection of curated structural variation in the human genome. Catalogue of human genomic structural variation identified in healthy control samples for studies aiming to correlate genomic variation with phenotypic data. It is continuously updated with new data from peer reviewed research studies. The Database is no longer accepting direct submission of data as they are currently part of a collaboration with two new archival CNV databases at EBI and NCBI, called DGVa and dbVAR, respectively. One of the changes to DGV as part of this collaborative effort is that they will no longer be accepting direct submissions, but rather obtain the datasets from DGVa (short for DGV archive). This will ensure that the three databases are synchronized, and will allow for an official accessioning of variants.

Proper citation: Database of Genomic Variants (RRID:SCR_007000) Copy   

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http://www.cpc.unc.edu/projects/addhealth

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

Proper citation: Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Copy   

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http://aramemnon.botanik.uni-koeln.de

A database of putative membrane proteins of Thale Cress (Arabidopsis thaliana), Rice (Oryza sativa) and about some 6700 putative membrane proteins of ~300 other seed plants. The database stores data about: * protein, cDNA and genomic sequences * exon predictions (A.thaliana and O.sativa) * different cDNA/protein models of genes (A.thaliana and O.sativa) * ontology terms according to the Gene Ontology (GO) Consortium * protein sequence motifs as predictable by using the PFAM database * transporter classification as predictable by using the TC-system * bibliographic references * predictions for transmembrane spanning proteins (transmembrane alpha helices, beta barrels) * predictions for membrane-anchored proteins (GPI-attachment, prenylation, myristoylation) * prediction of the subcellular location * consensus predictions (transmembrane alpha helices, subcellular location) * isospecic homologs (''paralogs'') * heterospecic homologs (''orthologs'')

Proper citation: ARAMEMNON, a Novel Database for Arabidopsis Integral Membrane Proteins (RRID:SCR_007552) Copy   

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http://blocks.fhcrc.org

Blocks is a database of highly conserved regions of proteins, or Blocks. THe database is no longer maintained or updated and some of its tools are no longer functional. However, Blocks does provide Block Searcher, Get Blocks and Block Maker, aids to detection and verification of protein sequence homology. They compare a protein or DNA sequence to a database of protein blocks (current version), retrieve blocks, and create new blocks, respectively. Users can further view blocks by (keyword or number), search a sequence against the database of blocks, search blocks against each other, or make blocks of their own.

Proper citation: Blocks (RRID:SCR_007567) Copy   

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http://urgv.evry.inra.fr/CATdb

CATdb collects together all the information on transcriptome experiments done at URGV with CATMA micro arrays. All data in CATdb come from the URGV micro array platforms. Common procedures are used including any steps from the experiment design to the statistical analyses. Directed through a WEB interface, biologists enter the standard description of each experimental step (extraction, labelling, hybridization and scanning). Then, normalization and statistical analyses are done following a set of selected methods depending on the experimental design and array types.

Proper citation: CATdb: a Complete Arabidopsis Transcriptome database (RRID:SCR_007582) Copy   

•   Source: SciCrunch Registry