14 Mar 2012

Learning about Genes and Their Products

These resources give a general overview of a gene, along with some of the following information: Official symbol, locus, associated disorders or traits, mode of inheritance, name and function of gene product, and links to additional gene-specific resources.

Overview: Created and edited by Victor A. McKusick, MD and his colleagues at Johns Hopkins School of Medicine, OMIM is a large, searchable, up-to-date database of human genes, genetic traits, and disorders. In addition to summarizing what is known about a particular gene, trait, or disorder, each record also contains reference material and links to other NCBI resources such as literature citations in MEDLINE and related sequence records. OMIM is intended for use by genetics researchers, advanced life-science students, and healthcare professionals concerned with genetic disorders. The database is updated daily. Three different interfaces are provided for exploring particular genes and genetic conditions: Search, Gene Map, and Morbid Map. An article on OMIM is available from the NCBI Bookshelf.

Search Tips: Browse an alphabetical listing of genetic disorders featured in OMIM with Morbid Map. View a listing of genes organized by cytogenetic location using OMIM's Gene Map. Search for information about specific genes, traits, or disorders using OMIM's Search options. For step-by-step instructions describing how to search OMIM, see our OMIM Search Tutorial. Additional information about searching OMIM is available from the Help and FAQs pages.

Information Provided: Some of the types of information provided in OMIM records include: Genes that have been linked to disorders, the official symbol for a gene, key mutations in genes that result in disease, functions of genes and the proteins they encode, as well as descriptions of genetic conditions and how they are inherited. Links to citations in Medline, related OMIM entries and entries in other NCBI databases also are included. The amount of information included in each entry depends upon how much researchers know about a particular gene or condition.

Overview: LocusLink is an NCBI database that serves as a single query interface to gene-specific information from a wide variety of bioinformatics sources. LocusLink includes descriptive information about genetic loci in human, cow, fruit fly, mouse, rat, nematode, zebrafish, and human immunodeficiency virus type 1 genomes.

Search Tips: Users can query LocusLink by typing keywords (such as disease or protein name, gene symbol, accession numbers, or other database ID numbers) into the search box at the top of the main page. Query options include truncation of terms using the asterisk (*) as a wild card, field restriction, and use of Boolean operators (and, or, not) that are not case sensitive. Grouping phrases by parentheses or quotation marks is not supported.

LocusLink has a system of controlled terms that can be used to retrieve only those records with a particular feature. One of the controlled terms is disease_known, which will return only loci associated with a known disorder. See the Query Tips in the Help file for a complete listing and more detailed descriptions of controlled terms. For more on searching LocusLink, see the Help file. LocusLink also provides a FAQ page.

Information Provided: Each LocusLink report may include the following types of information: Links to gene-specific entries in other databases, official gene nomenclature, LocusID (identification number assigned to the gene by LocusLink), overview of protein function, alternate symbols and aliases, phenotypes or expressed characteristics associated with the gene, other database ID numbers, similar genes from other genomes, links to cytogenetic maps, links to sequence records, and links to other related information sources.

Overview: Developed at the Weizmann Institute of Science in Israel, GeneCards is a database of human genes, their products, and their involvement in hereditary disorders. GeneCards automatically extracts gene-specific information from a variety of Web-based bioinformatics resources and integrates the data into each entry. The database was designed for scientists who want to use one interface to access multiple databases for information about human genes that have been assigned approved symbols.

Search Tips: Users can search GeneCards by keyword or gene symbol/alias using the search box on the home page. Keywords can be single or multiple terms, GenBank accession number, chromosome number, or gene locus. Truncation using an asterisk (*) as a wild card at the beginning or end of a search term is supported. The Boolean operators AND and OR can be used to connect terms. The Boolean operator NOT is not supported. Examples are provided for keyword searching. Users may also browse a complete listing of genes or a subset of disease genes featured in GeneCards. To learn more about searching GeneCards, check out Quick Start, Guided Tour and The GeneCards Guidance System.

Information Provided: Each GeneCard may include the following information: Official gene name and symbol, synonyms or alternative names, ID numbers assigned to the gene in other databases, chromosomal location, chromosome map showing where the gene is found, domains and protein families associated with the gene's protein product, links to sequence records, expression patterns in human tissues, links to similar genes in other organisms, SNPs and variants, disorders and mutations, links to citations in Medline, and links to other related resources. Each GeneCard also links to sources used to create the entry. GeneCards encourages feedback from its users and provides a form for submitting comments and suggestions.

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