Searching across hundreds of databases
High-throughput technologies have led to the rapid generation of large-scale datasets about genes and gene products. These technologies have also shifted our research focus from 'single genes' to 'gene sets'. We have developed a web-based integrated data mining system, WebGestalt (http://genereg.ornl.gov/webgestalt/), to help biologists in exploring large sets of genes. WebGestalt is composed of four modules: gene set management, information retrieval, organization/visualization, and statistics. The management module uploads, saves, retrieves and deletes gene sets, as well as performs Boolean operations to generate the unions, intersections or differences between different gene sets. The information retrieval module currently retrieves information for up to 20 attributes for all genes in a gene set. The organization/visualization module organizes and visualizes gene sets in various biological contexts, including Gene Ontology, tissue expression pattern, chromosome distribution, metabolic and signaling pathways, protein domain information and publications. The statistics module recommends and performs statistical tests to suggest biological areas that are important to a gene set and warrant further investigation. In order to demonstrate the use of WebGestalt, we have generated 48 gene sets with genes over-represented in various human tissue types. Exploration of all the 48 gene sets using WebGestalt is available for the public at http://genereg.ornl.gov/webgestalt/wg_enrich.php.
Pubmed ID: 15980575 RIS Download
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Multi species reference database. Comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.
View all literature mentionsCollection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
View all literature mentionsComputable knowledge regarding functions of genes and gene products. GO resources include biomedical ontologies that cover molecular domains of all life forms as well as extensive compilations of gene product annotations to these ontologies that provide largely species-neutral, comprehensive statements about what gene products do. Used to standardize representation of gene and gene product attributes across species and databases.
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023.Software tools that have been developed by AT&T Labs researchers. In addition to the software tools available through Open Source and Non-Commercial licenses as listed on this page, AT&T has additional software and technology solutions available for licensing. Please reference the individual project web pages for specific license agreements. If an available license agreement does not meet your needs, please contact attip (at) att.com for assistance with a customized license. Open Source Licenses * AST: Advanced Software Technologies Open Source Collection * Cdt: Container Data Types Library * ECharts: A state machine-based programming language * GGobi: Data visualization for high-dimensional data * GSDjVu/DjVuDigital: Ghostscript driver to convert PS and PDF files to DjVu files * Graphviz: Tools for viewing and interacting with graph diagrams * PADS: Processing Arbitrary Data Streams * Sfio: Portable library for performing I/O * UWIN: Unix on Windows 95 and NT Machines * Vcodex: Software package for data transformation * WSP: Web Scraping Proxy * Yoix: The Yoix Scripting Language and Interpreter * iPlots: Interactive graphics for data analysis in R * vmalloc: Region Memory Allocator Non-Commercial Binary Licenses * BoosTexter: A general purpose machine-learning program * Hancock: A language for processing large-scale data Non-Commercial Source Licenses * ASDT: The AT&T Statistical Dialog Toolkit (ASDT) * Hancock: A language for processing large-scale data
View all literature mentionsProject to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools
View all literature mentionsCollection of curated, non-redundant genomic DNA, transcript RNA, and protein sequences produced by NCBI. Provides a reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis, expression studies, and comparative analyses. Accessed through the Nucleotide and Protein databases.
View all literature mentionsDatabase for genomes that have been completely sequenced, have active research community to contribute gene-specific information, or that are scheduled for intense sequence analysis. Includes nomenclature, map location, gene products and their attributes, markers, phenotypes, and links to citations, sequences, variation details, maps, expression, homologs, protein domains and external databases. All entries follow NCBI's format for data collections. Content of Entrez Gene represents result of curation and automated integration of data from NCBI's Reference Sequence project (RefSeq), from collaborating model organism databases, and from many other databases available from NCBI. Records are assigned unique, stable and tracked integers as identifiers. Content is updated as new information becomes available.
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