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COXPRESdb: a database of coexpressed gene networks in mammals.

Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K - Nucleic Acids Res. (2007)

Bottom Line: A database of coexpressed gene sets can provide valuable information for a wide variety of experimental designs, such as targeting of genes for functional identification, gene regulation and/or protein-protein interactions.Coexpressed gene databases derived from publicly available GeneChip data are widely used in Arabidopsis research, but platforms that examine coexpression for higher mammals are rather limited.When the networks became too big for the static picture on the web in GO networks or in tissue networks, we used Google Maps API to visualize them interactively.

View Article: PubMed Central - PubMed

Affiliation: Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan.

ABSTRACT
A database of coexpressed gene sets can provide valuable information for a wide variety of experimental designs, such as targeting of genes for functional identification, gene regulation and/or protein-protein interactions. Coexpressed gene databases derived from publicly available GeneChip data are widely used in Arabidopsis research, but platforms that examine coexpression for higher mammals are rather limited. Therefore, we have constructed a new database, COXPRESdb (coexpressed gene database) (http://coxpresdb.hgc.jp), for coexpressed gene lists and networks in human and mouse. Coexpression data could be calculated for 19 777 and 21 036 genes in human and mouse, respectively, by using the GeneChip data in NCBI GEO. COXPRESdb enables analysis of the four types of coexpression networks: (i) highly coexpressed genes for every gene, (ii) genes with the same GO annotation, (iii) genes expressed in the same tissue and (iv) user-defined gene sets. When the networks became too big for the static picture on the web in GO networks or in tissue networks, we used Google Maps API to visualize them interactively. COXPRESdb also provides a view to compare the human and mouse coexpression patterns to estimate the conservation between the two species.

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An example of the listing for genes related to virus-response using COXPRESdb. The thin red circles in (A), (B) and (C) indicate the link to the next step indicated by green arrows. (A) Top page. (B) Keyword search result. The ‘list’ is linked to the list of the genes including the GO term and all GO subcategory terms. The ‘network’ is linked to the GO network page. (C) GO network page. See text for details. (D) Results of the coexpressed gene search. Gene symbols in the pink box indicate query genes from the previous step.
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Figure 2: An example of the listing for genes related to virus-response using COXPRESdb. The thin red circles in (A), (B) and (C) indicate the link to the next step indicated by green arrows. (A) Top page. (B) Keyword search result. The ‘list’ is linked to the list of the genes including the GO term and all GO subcategory terms. The ‘network’ is linked to the GO network page. (C) GO network page. See text for details. (D) Results of the coexpressed gene search. Gene symbols in the pink box indicate query genes from the previous step.

Mentions: An example of the estimation of gene functions using COXPRESdb. The thin red circles in (A), (B) and (C) indicate the link to the next step indicated by green arrows. (A) Top page. (B) Keyword search result. (C) Gene page for ACTR3. In the functional annotation section, the ‘list’ is linked to the list of genes, including the GO term and all GO subcategory terms. The ‘network’ is linked to GO network page (see Figure 2C). When a GO annotation is linked to any publication, the GO evidence codes (TAS and IPI in this example) of the GO annotation is linked to a corresponding PubMed page. The ‘ortholog page’ is linked to the page for parallel view of the gene page for this gene and its mouse ortholog. Small icons on the right side of the page are external links. Subcellular localizations are predicted by WoLF PSORT software, the score for which is scaled from 0 (less reliable) to 10 (most reliable), in integers. In the coexpression section, a coexpression network for the 20 highest coexpressed genes to the query gene is provided. The network consists of nodes and edges. Each node represents a coexpressed gene, which works as a link to the corresponding gene page, and each edge indicates the strength of coexpression by its thickness (see DATA SOURCES AND CALCULATIONS for details). The shaded node highlights the current gene, and the red edges, if any, indicate existence of reported PPIs according to the HPRD annotation (14). The orange edges indicate the existence of strong coexpression between the corresponding orthologs in mouse. The gene list is located in a table next to the network. The value of each expression pattern similarity (ExSim) in the table is highlighted by red colour corresponding to the edge thicknesses. The ‘detail’ in the table is linked to the coexpression viewer, which illustrates the contribution of each sample to the expression pattern similarity. See the text for the explanation of the other section shown. (D) Tissue-specific network page for neutrophils. ACTR3 is marked with a yellow symbol.


COXPRESdb: a database of coexpressed gene networks in mammals.

Obayashi T, Hayashi S, Shibaoka M, Saeki M, Ohta H, Kinoshita K - Nucleic Acids Res. (2007)

An example of the listing for genes related to virus-response using COXPRESdb. The thin red circles in (A), (B) and (C) indicate the link to the next step indicated by green arrows. (A) Top page. (B) Keyword search result. The ‘list’ is linked to the list of the genes including the GO term and all GO subcategory terms. The ‘network’ is linked to the GO network page. (C) GO network page. See text for details. (D) Results of the coexpressed gene search. Gene symbols in the pink box indicate query genes from the previous step.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238883&req=5

Figure 2: An example of the listing for genes related to virus-response using COXPRESdb. The thin red circles in (A), (B) and (C) indicate the link to the next step indicated by green arrows. (A) Top page. (B) Keyword search result. The ‘list’ is linked to the list of the genes including the GO term and all GO subcategory terms. The ‘network’ is linked to the GO network page. (C) GO network page. See text for details. (D) Results of the coexpressed gene search. Gene symbols in the pink box indicate query genes from the previous step.
Mentions: An example of the estimation of gene functions using COXPRESdb. The thin red circles in (A), (B) and (C) indicate the link to the next step indicated by green arrows. (A) Top page. (B) Keyword search result. (C) Gene page for ACTR3. In the functional annotation section, the ‘list’ is linked to the list of genes, including the GO term and all GO subcategory terms. The ‘network’ is linked to GO network page (see Figure 2C). When a GO annotation is linked to any publication, the GO evidence codes (TAS and IPI in this example) of the GO annotation is linked to a corresponding PubMed page. The ‘ortholog page’ is linked to the page for parallel view of the gene page for this gene and its mouse ortholog. Small icons on the right side of the page are external links. Subcellular localizations are predicted by WoLF PSORT software, the score for which is scaled from 0 (less reliable) to 10 (most reliable), in integers. In the coexpression section, a coexpression network for the 20 highest coexpressed genes to the query gene is provided. The network consists of nodes and edges. Each node represents a coexpressed gene, which works as a link to the corresponding gene page, and each edge indicates the strength of coexpression by its thickness (see DATA SOURCES AND CALCULATIONS for details). The shaded node highlights the current gene, and the red edges, if any, indicate existence of reported PPIs according to the HPRD annotation (14). The orange edges indicate the existence of strong coexpression between the corresponding orthologs in mouse. The gene list is located in a table next to the network. The value of each expression pattern similarity (ExSim) in the table is highlighted by red colour corresponding to the edge thicknesses. The ‘detail’ in the table is linked to the coexpression viewer, which illustrates the contribution of each sample to the expression pattern similarity. See the text for the explanation of the other section shown. (D) Tissue-specific network page for neutrophils. ACTR3 is marked with a yellow symbol.

Bottom Line: A database of coexpressed gene sets can provide valuable information for a wide variety of experimental designs, such as targeting of genes for functional identification, gene regulation and/or protein-protein interactions.Coexpressed gene databases derived from publicly available GeneChip data are widely used in Arabidopsis research, but platforms that examine coexpression for higher mammals are rather limited.When the networks became too big for the static picture on the web in GO networks or in tissue networks, we used Google Maps API to visualize them interactively.

View Article: PubMed Central - PubMed

Affiliation: Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan.

ABSTRACT
A database of coexpressed gene sets can provide valuable information for a wide variety of experimental designs, such as targeting of genes for functional identification, gene regulation and/or protein-protein interactions. Coexpressed gene databases derived from publicly available GeneChip data are widely used in Arabidopsis research, but platforms that examine coexpression for higher mammals are rather limited. Therefore, we have constructed a new database, COXPRESdb (coexpressed gene database) (http://coxpresdb.hgc.jp), for coexpressed gene lists and networks in human and mouse. Coexpression data could be calculated for 19 777 and 21 036 genes in human and mouse, respectively, by using the GeneChip data in NCBI GEO. COXPRESdb enables analysis of the four types of coexpression networks: (i) highly coexpressed genes for every gene, (ii) genes with the same GO annotation, (iii) genes expressed in the same tissue and (iv) user-defined gene sets. When the networks became too big for the static picture on the web in GO networks or in tissue networks, we used Google Maps API to visualize them interactively. COXPRESdb also provides a view to compare the human and mouse coexpression patterns to estimate the conservation between the two species.

Show MeSH