Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomy and development of different species. Then, in order to perform automated cross species comparisons, homology relationships across anatomies, and comparison criteria between developmental stages, are designed. Data can be retrieved by ontology browsing, textual search, expression search, or advanced expression search. Gene expression patterns can be compared by selecting any gene family (e.g. ENSFM00500000270089). The full content of the Bgee expression database, the ontologies, the homology links between anatomical ontologies, and the relationships between developmental ontologies, are all available in the download section. More information is provided in the documentation. All data sources used in Bgee are listed on the data sources page. ... [Information of the supplier]
Cancer GEnome Mine is a public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes. CanGEM supports the MIAME standard and in addition, stores clinical information using standardized controlled vocabularies whenever possible. Microarray probes are re-annotated with their physical coordinates in the human genome and aCGH data is analyzed to yield gene-specific copy numbers. Users can build custom datasets by querying for specific clinical sample characteristics or copy number changes of individual genes. Aberration frequencies can be calculated for these datasets, and the data can be visualized on the human genome map with gene annotations. Furthermore, the original data files are available for more detailed analysis. ... [Information of the supplier, modified]
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 Open Tiger Genome Project is a public service launched by a non-profit foundation Genome Research Foundation (GRF) and TheragenEtex Inc. It is aming at preserving tiger genome information, the level 1 endangered species designated by the Korean Ministry of Environment. Genome Research Foundation is pursuing to complete the standard reference genome of Amur (Korean or Siberian) tiger by sequencing and analyzing its genome. ... [Information of the supplier]
In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. [Source: http://nar.oxfordjournals.org/content/early/2011/11/15/nar.gkr1007.full] ... [Miscellaneous as indicated]
Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromesome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to cooresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. It is free to browse and download data in Dr.VIS. ... [Information of the supplier]
Ascertaining when and where genes are expressed is of crucial importance in order to understand the physiological role of a given gene/protein and the interactions between them. In addition, the normal expression patterns can then be compared to those observed in a variety of pathological conditions to identify pathological hallmarks of gene expression. The EURExpress, an integrated project funded by the EU under the VI Framework proposes a transcriptome-wide acquisition of expression patterns chiefly by means of in situ hybridization (ISH) with non-radioactive probes and will use this data to establish a web-linked, interactive digital transcriptome atlas of embryonic mouse. The final goal of the project is to create the expression data of > 20,000 genes by RNA in situ hybridization on sagittal sections from E14.5 wild type murine embryos. This data will result in a detailed description (at a cellular level) of gene expression patterns in the developing mouse. The “transcriptome atlas” will be generated using a newly developed automated RNA in situ hybridization system. Automated scanning microscopes will collect image data, which will be electronically sent out in a digital format for annotation. The latter will be performed using a web-based “virtual” microscope and be entered in a hierarchical database specifically designed to hold large amounts of image data and display them in a user-friendly format. For a subset of genes, mainly those directly involved in human diseases, expression data will also be generated by using human and murine tissue arrays. This will offer the opportunity to compare human and mouse expression patterns in adult tissues. This project builds on a strong European concentration of skills in gene expression analysis and mouse genomics and integrates European skills, efforts, resources and information in the field of systematic gene expression analysis. All expression data generated by EURExpress will be made readily available to the scientific community via the EURExpress web-linked database, considerably advancing our knowledge of gene function and having a significant impact on the identification of gene expression markers of disease processes. ... [Information of the supplier]
This database presents the current results of large scale protein trapping screens that provide both information on which cells express each tagged gene, and subcellular localization of GFP-tagged proteins. It contains sequence coordinates of inserted transposons, information on the tagged genes, and images with expression patterns of GFP in Drosophila tissues. FlyTrap serves as the data repository for lines generated in the Chia, Cooley, and Spradling labs. The protein trap stocks listed in FlyTrap are available for distribution. ... [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]
In September, 2001, the National Institute of Diabetes, Digestive, and Kidney Diseases (NIDDK) convened a working group of its National Advisory Council to develop a strategic plan for Stem Cells and Developmental Biology. The working group made several recommendations, with the overall goals of providing new strategies for repairing or replacing damaged organs and generating new insights into pathologic processes underlying developmental defects and disease. There is the need for a more thorough understanding of organogenesis so that tissue degeneration and congenital malformations might be prevented and treated. The goal of GUDMAP is a fundamental description of the developing kidney and GU tract. The panel recommended that the following three objectives be combined to form the GUDMAP. a) High throughput in situ hybridization analyses to define the expression pattern of genes expressed in the developing kidney and GU tract, b) High resolution gene expression analyses to define gene expression during developmental time, the overlap in gene expression patterns, and the correlation between boundaries of gene expression and boundaries of anatomic or functional domains and c) Development of a database to house and annotate the above data and to provide rapid access of this data to the entire research community. Microarray analyses and the generation of murine strains with genetic markers are also goals of GUDMAP which serve to bolster the overall aim of defining molecular and cellular anatomy through developmental time. ... [Information of the supplier, modified]
