The HuGE Literature Finder is one component of the HuGE Navigator, an integrated, searchable knowledge base of genetic associations and related information in human genome epidemiology. In 2001, HuGENet launched the HuGE Published Literature database (HuGE Pub Lit), a continually updated and accessible knowledge base on the World Wide Web that tracks the growing published literature of human genome epidemiologic studies. HuGE Pub Lit offers a starting point for assembling articles for meta-analysis, highlighting research gaps, suggesting applied research questions, and identifying potential collaborators. HuGE Pub Lit contains links to abstracts on PubMed that meet the inclusion and exclusion criteria (see below). HuGENet research staff is responsible for extracting relevant articles from PubMed and entering them into the HuGE Pub Lit database on a weekly basis. Since June 2007, a new automatic HuGE literature screening – GAPscreener was implemented to assist the weekly HuGE literature scanning from PubMed. The sensitivity of HuGE literature screening performance can reach 97.5%. An average of 500 new articles per week is retrieved by GAPscreener. A researcher who is familiar with the eligibility criteria for human genome epidemiology then reviews each title and abstract (or in a few cases, the full text). This researcher decides whether the study will be included in the database and, if it will, assigns indexing for each article. HuGE Literature Finder is a newly-designed HuGE Pub Lit database that utilizes the Unified Medical Language System (UMLS) as an indexing mechanism. ... [Information of the supplier]
H-DBAS is a unique database of alternative splicing (AS) based on H-InvDB. The features of H-DBAS is as follows: 1) Representative AS variants (RASVs) were identified from 8 data sets consist of 6 mammalian model organisms (human, mouse, rat, chimpanzee, macaque and dog). The contents of data sets and the corresponding species are as follows: Full-length cDNA data set, mRNA data set, RNA data set 2) Equally-spliced variants (ESVs) were identified from RASVs between human and mouse, rat, chimpanzee, macaque and dog by using comparative genomics. Splice sites and splice motifs affecting SNPs can be observed in human. 3) RASVs affecting protein functions (protein motif, GO, subcellular localization signal and transmembrane domain) can be observed in human. 4) AS junctions expressed in specified cellular fractions (cytoplasm, nuclear and polysome) of human cell were detected by using RNA-Seq tags. The translation validation of the variants having AS junctions were analyzed by compared with RefSeq junctions. The results are shown from RNA-Seq analysis page. ... [Information of the supplier]
GWAS Central (previously the Human Genome Variation database of Genotype-to-Phenotype information) is a database of summary level findings from genetic association studies, both large and small. We actively gather datasets from public domain projects, and encourage direct data submission from the community. GWAS Central is built upon a basal layer of Markers that comprises all known SNPs and other variants from public databases such as dbSNP and the DBGV. Allele and genotype frequency data, plus genetic association significance findings, are added on top of the Marker data, and organised the same way that investigations are reported in typical journal manuscripts. Critically, no individual level genotypes or phenotypes are presented in GWAS Central – only group level aggregated (summary level) data. The largest unit in a data submission is a Study, which can be thought of as being equivalent to one journal article. This may contain one or more Experiments, one or more Sample Panels of test subjects, and one or more Phenotypes. Sample Panels may be characterised in terms of various Phenotypes, and they also may be combined and/or split into Assayed Panels. The Assayed Panels are used as the basis for reporting allele/genotype frequencies (in `Genotype Experiments`) and/or genetic association findings (in ‘Analysis Experiments’). Environmental factors are handled as part of the Sample Panel and Assayed Panel data structures. ... [Information of the supplier]
SNPedia is a wiki-based bioinformatics web site that serves as a database of single nucleotide polymorphisms (SNPs). Each article on a SNP provides a short description, links to scientific articles and personal genomics web sites, as well as microarray information about that SNP. [Information of the supplier]
WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. [Information of the supplier]
The cyclic AMP response element (CRE)-binding protein (CREB) family of activators (CREB1, CREM, ATF1) functions in diverse physiological processes, including the control of cellular metabolism, growth-factor-dependent cell survival, and developement an plasticity of neurons. A diverse range of signals, including cAMP, calcium, stress and mitogenic stimuli, can activate CREB and promote target gene expression. This database is dedicated to catogerize CREB target genes in a comprehensive and easy-to-search way. We have used a multi-layered approach to predict, validate and chracterize CREB target genes. For each gene, we try to provide the following information: 1. CREB binding sites on the promoters, 2. Promoter occupancy by CREB, 3. Gene activation by cAMP in tissues. The data are for humans, rats, and mice. ... [Information of the supplier, modified]
The Genetic Association Database is an archive of human genetic association studies of complex diseases and disorders. The goal of this database is to allow the user to rapidly identify medically relevant polymorphism from the large volume of polymorphism and mutational data, in the context of standardized nomenclature. ... [Information of the supplier]
T1DBase is a public website and database that supports the type 1 diabetes (T1D) research community. It is being created by a joint effort between the Institute for Systems Biology, Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory and the Juvenile Diabetes Research Foundation International. T1DBase collects information from public sources and from collaborating laboatories, integrates this information, and presents it in a form that is useful for T1D researchers. The current data scope includes annotated genomic sequences for suspected T1D susceptibility regions; microarray data; functional annotation of genes active in beta cells; and "global"datasets, generally from the literature, that are useful for systems biology studies. ... [Information of the supplier, modified]
The Interactive Fly - a cyberspace guide to Drosophila development and metazoan evolution - was first released July/August 1996, with updates provided at approximately one month intervals, through September 1997 (edition 13). Updating quarterly started with edition 14. With edition 40, the Interactive Fly began to schedule updates three times a year: fall, winter and spring. ... [Information of the supplier, modified]
FlyView is an image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes). Our aim is to establish the possibility to compare images on the computer screen and to search for special patterns at different developmental stages. FlyView presents three possibilities for searching: Search for pattern elements (with keywords in text descriptions, getting back images with links to the appropriate stocks), search for stocks (with stock number, allele, genotype, chromosome, insertion site, viability, developmental stage or expression pattern, getting back a list of found stocks that guide to full descriptions (including links to images, e-mail address for ordering and, in the case of BDGP lines, also direct links to FlyBase and/or EofD)) and Overview (an actual list of all lines included in FlyView, linked to stock descriptions and images). The success of this database exclusively depends on the activity of the Drosophila community. All Drosophila workers are asked to contribute to this database by submitting images and accompanying text. ... [Information of the supplier, modified]
