CO-eXPRESsed gene database (COXPRESdb)

Category Genomics>Gene Expression Databases/Tools

Abstract COXPRESdb is a database of co-expressed 'gene networks' in mammals. COXPRESdb consists of co-expressed gene lists and networks in both human and mouse species.

Co-expression data can be calculated for 19,777 and 21,036 genes in human and mouse, respectively, by using the GeneChip data in NCBI GEO (see G6G Abstract 20013).

COXPRESdb provides co-expressed gene networks and co-expressed gene lists 'ordered by' the strength of co-expression for both human and mouse species.

COXPRESdb enables the analysis of four (4) types of 'co-expression gene networks' –

1) Highly co-expressed genes for every gene,

2) genes with the same Gene Ontology (GO) annotation,

3) genes expressed in the same tissue and

4) user-defined gene sets.

When the gene networks became too big for a static picture on the web for GO networks or for tissue networks, the manufacturer used Google Maps API to visualize them interactively.

COXPRESdb also provides a cross-species view to compare the co- expression networks in both the human and mouse species because conserved co-expression patterns may enhance the reliability of the co- expressed network and they can be used to identify possible protein- protein interactions (PPIs) more effectively.

Notably, the known PPIs in the Human Protein Reference Database (HPRD) are also shown in the co-expression networks.

COXPRESdb consists of three (3) types of pages: 'gene page', 'GO network page' and a 'tissue-specific network page'.

COXPRESdb gene page --

The gene page is the central page, which is constructed for every gene defined by the National Center for Biotechnology Information (NCBI) Entrez database regardless of the existence of gene expression data.

The gene page is composed of three (3) sections: 1) functional annotation, (2) gene co-expression and (3) gene expression.

The names of each part are highlighted by green bars on the gene page.

Each gene page has a URL, so that an external database can be directly linked to this page.

1) The 'functional annotation' section provides functional gene annotations obtained from NCBI, GO and Kyoto Encyclopedia of Genes and Genomes (KEGG), as well as protein subcellular localization predicted by WoLF PSORT.

2) The 'gene co-expression' section provides the co-expressed gene network(s) relevant to this gene. The gene page lists the 20 most highly co-expressed genes based on expression pattern similarity.

Only the top 20 genes are shown because the expression similarity rapidly decreases after the top 20 genes, on average, and a large number of elements in a 'single network' are difficult to see on a single web page.

A list of the top 300 co-expressed genes is also available to find any other related genes, and thus the user has the ability to draw the network containing more genes with a network drawing tool provided by COXPRESdb (see below...).

The details of the co-expression can be seen by following the links to the ‘co-expression detail’. To focus on the co-expression network for each tissue, 'tissue-specific network pages' are available.

3) The 'gene expression' section shows the gene expression pattern(s) of the corresponding probe-set(s). The tissue-specific gene expression pattern is also shown.

To compare the gene info for orthologous gene sets, 'ortholog pages' are prepared in which the info in the gene page for human and from the corresponding mouse gene page are presented in parallel.

To identify the homologous gene set, the manufacturer used HomoloGene data, in which 16,981 gene sets were defined.

COXPRESdb GO network page --

A GO network page is constructed for each GO term. The 30 most highly co-expressed genes are selected, and their networks are drawn in parallel views for both human and mouse species.

The GO networks as well as 'tissue-specific networks' are constructed based on the same co-expression data as presented in the gene page, and the difference is in the selection of genes to be drawn.

There are 6,623 GO terms, and the networks are depicted as 1,820 GO terms. The other terms are Not considered because they have No highly co-expressed gene pairs with 'mutual rank' (MR) less than 50.

COXPRESdb tissue-specific network page --

The tissue-specific network page is constructed for 63 human tissues using the annotation of gene expression in HPRD.

The global picture of a co-expressed gene network in a tissue is too large to be visualized in a single picture on a static page, and therefore the manufacturer employed Google Maps API (Application Programming Interface) to interactively navigate these huge co- expression networks.

COXPRESdb Tools --

1) COXPRESdb NetworkDrawer tool - This tool draws a co-expressed gene network for user-defined genes. Input is Entrez Gene IDs.

2) COXPRESdb HCluster tool - This tool does hierarchical clustering for user-defined genes. Input is Entrez Gene IDs.

3) COXPRESdb CoexViewer - co-expression viewer tool - This tool returns a scatter plot of co-expression between two genes. Input is two (2) Entrez Gene IDs.

4) COXPRESdb ExViewer - Expression viewer tool - This tool returns an expression pattern for the user-defined input gene. Input is an Entrez Gene ID for human or mouse species.

5) COXPRESdb GOPathDrawer tool - Drawing hierarchical structures of Gene Ontology (GO) terms - This tool draws hierarchical structures of user-defined GO terms.

COXPRESdb also provides various Search capabilities and covers additional species.

System Requirements



Manufacturer Web Site COXPRESdb

Price Contact manufacturer.

G6G Abstract Number 20481

G6G Manufacturer Number 104106