a database management system for understanding plant gene function by associating between co-expressed genes and biological processes in plants. Information on biological processes is based on Gene Ontology biological process. CoP is composed of multiple databases that are based on information about gene co-expression, specific gene expression, biological process, metabolic pathway and are mutually interconnected. The omics data in CoP were obtained from the NCBI, TAIR, and GRAMENE databases. Co-expression analyses in CoP were executed using the Confeito algorithm (Ogata et al., Genome Informatics , 23:117-127, 2009; not yet available on line), an approach based on co-expression network analysis. Click here for more info. |
To display a co-expression network in the page of a co-expression module,
the SVG viewer is required. |
has been released at November 11th, 2009. |
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| 5257 assays of Arabidopsis thaliana | |
| 95 assays of poplar (Populus trichocarpa) | |
| 2994 assays of soy bean (Glycine max) | |
| 403 assays of barley (Hordeum vulgare) | |
| 432 assays of rice (Oryza sativa) | |
| 368 assays of wheat (Triticum aestivum) | |
| 210 assays of grape (Vitis vinifera) | |
| 263 assays of maize (Zea mays). | |
| Data sources for this version | |
Arabidopsis genes: TAIR9_functional_description, dated at 20090702 |
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Arabidopsis GO terms: gene_association.tair, dated at 20091028 |
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Rice GO terms: gene_association.gramene_oryza, dated at 20090924 |
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For Arabidopsis co-expression analysis, an approach using experiments in which genes are specifically expressed has been added. |
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present a co-expression analysis in the different design of poplar microarray data and a mode to search genes that are specifically expressed in multiple experiments. |
20071128 |
CoexProcess, the previous version, was published. |
20090312 |
CoP, the present version, was published; including Arabidopsis co-expression analyses using 5257, 3654, and 1388 assays of DNA microarray dataset and poplar co-expression analysis using 95 assays. |
20090608 |
Soybean co-expression analysis using 2994 assays and Arabidopsis co-expression analysis using expression data obtained by experiments in which genes were specifically expressed were added. |
20091111 |
Rice, barley, wheat, grape, and maize co-expression analyses were added. |
20100117 |
Statistical indices for co-expression modules were added. |
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