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BGEM: an in situ hybridization database of gene expression in the embryonic and adult mouse nervous system.

PLoS biology | Apr 10, 2006

Pubmed ID: 16602821 RIS Download

Mesh terms: Animals | Brain | Databases, Genetic | Gene Expression Profiling | Humans | In Situ Hybridization | Internet | Mice | Mice, Inbred C57BL | Molecular Sequence Data | Nervous System

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This is a list of tools and resources that we have found mentioned in this publication.


GO

A community-based bioinformatics resource consisting of three structured controlled vocabularies (ontologies) for the annotation of gene products with respect to their molecular function, cellular component, and biological role in a species-independent manner. This initiative to standardize the representation of gene and gene product attributes across species and databases is an effort to address the need for consistent descriptions of gene products in different databases. The Gene Ontology project encourages input from the community into both the content of the GO and annotation using GO. There are three separate aspects to this effort: first, they write and maintain the ontologies themselves; second, they make cross-links between the ontologies and the genes and gene products in the collaborating databases; and third, they develop tools that facilitate the creation, maintenance and use of ontologies. The controlled vocabularies are structured so that users can query them at different levels: for example, uers can use GO to find all the gene products in the mouse genome that are involved in signal transduction, or users can zoom in on all the receptor tyrosine kinases. This structure also allows annotators to assign properties to gene products at different levels, depending on how much is known about a gene product.

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GenePaint.org

A digital atlas of gene expression patterns in the developing and adult mouse. Several reference atlases are also available through this site. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. Sections were labeled using non radioactive in situ hybridization with riboprobes and annotated for level of gene expression (not detected, weak, medium, strong) and pattern (ubiquitous, regional, scattered). Sections are available from several developmental ages: E10.5, E14.5 (whole embryos), E15.5, P7 and P56 (brains only). To retrieve expression patterns, search by gene name, site of expression, GenBank accession number or sequence homology. For viewing expression patterns, GenePaint.org features a virtual microscope tool that enables zooming into images down to cellular resolution.

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