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New features and content added to COMBREX

Below are brief descriptions of some of the new features and content that have been added to COMBREX with the May 6th 2011 update.

Documented phenotype data associated with genes

COMBREX now contains a “Phenotype data” section within gene detail pages which contains information about documented phenotypes associated with a gene of interest. Specifically, phenotype name, a brief description of the phenotype, expression class (e.g. wild type, knockout, etc.), and a link to the reference which documents the association of the gene with the listed phenotype are listed in this section. Currently, this phenotype data consists of antibiotic resistance, antibiotic hypersensitivity, and gene essentiality. Please refer to the FAQ section on Phenotype data.

Users can search for clusters containing genes associated with a specific phenotype using the options available in advanced search. Users can also view a list of all the phenotypes available in COMBREX by following the “View list of phenotypes” link within the advanced search options.

Identification of proteins that have been cloned and/or purified for experimentation

COMBREX now contains information about proteins that have been cloned and proteins that have been purified by a participant in the Protein Structure Initiative (PSI). The cloning and purification of these proteins are two steps in a series of experimental steps taken to determine their structures using NMR or X-ray crystallography.

Clusters containing proteins that been cloned and/or purified and genes encoding proteins that have been cloned and/or purified are marked with the

C
and
U
symbols, respectively. Please refer to the Glossary of terms and icons document in the help center. In addition users can also search specifically for clusters containing genes encoding cloned and/or purified proteins using the newly available options in advanced search.

NCBI Supercluster information

COMBREX now provides information on NCBI Superclusters. NCBI superclusters are a clique of NCBI related clusters. More info on related clusters can be found in the FAQ.

Users can access supercluster detail pages through cluster detail pages. For clusters within superclusters, i.e. those that have related clusters, there are links to the corresponding supercluster detail pages under the “summary” section in the cluster detail pages.

Downloading content from COMBREX

Users can now download content from COMBREX in Excel format. Currently, downloadable content include search results, a list of genes comprising a cluster, a list of clusters comprising a supercluster, a list of annotations of molecular function within a supercluster, and a list of genes associated with a certain phenotype.