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COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals

Coexpressed gene databases are valuable resources for identifying new gene functions or functional modules in metabolic pathways and signaling pathways. Although coexpressed gene databases are a fundamental platform in the field of plant biology, their use in animal studies is relatively limited. Th...

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Autores principales: Obayashi, Takeshi, Okamura, Yasunobu, Ito, Satoshi, Tadaka, Shu, Motoike, Ikuko N., Kinoshita, Kengo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531062/
https://www.ncbi.nlm.nih.gov/pubmed/23203868
http://dx.doi.org/10.1093/nar/gks1014
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author Obayashi, Takeshi
Okamura, Yasunobu
Ito, Satoshi
Tadaka, Shu
Motoike, Ikuko N.
Kinoshita, Kengo
author_facet Obayashi, Takeshi
Okamura, Yasunobu
Ito, Satoshi
Tadaka, Shu
Motoike, Ikuko N.
Kinoshita, Kengo
author_sort Obayashi, Takeshi
collection PubMed
description Coexpressed gene databases are valuable resources for identifying new gene functions or functional modules in metabolic pathways and signaling pathways. Although coexpressed gene databases are a fundamental platform in the field of plant biology, their use in animal studies is relatively limited. The COXPRESdb (http://coxpresdb.jp) provides coexpression relationships for multiple animal species, as comparisons of coexpressed gene lists can enhance the reliability of gene coexpression determinations. Here, we report the updates of the database, mainly focusing on the following two points. First, we updated our coexpression data by including recent microarray data for the previous seven species (human, mouse, rat, chicken, fly, zebrafish and nematode) and adding four new species (monkey, dog, budding yeast and fission yeast), along with a new human microarray platform. A reliability scoring function was also implemented, based on coexpression conservation to filter out coexpression with low reliability. Second, the network drawing function was updated, to implement automatic cluster analyses with enrichment analyses in Gene Ontology and in cis elements, along with interactive network analyses with Cytoscape Web. With these updates, COXPRESdb will become a more powerful tool for analyses of functional and regulatory networks of genes in a variety of animal species.
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spelling pubmed-35310622013-03-07 COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals Obayashi, Takeshi Okamura, Yasunobu Ito, Satoshi Tadaka, Shu Motoike, Ikuko N. Kinoshita, Kengo Nucleic Acids Res Articles Coexpressed gene databases are valuable resources for identifying new gene functions or functional modules in metabolic pathways and signaling pathways. Although coexpressed gene databases are a fundamental platform in the field of plant biology, their use in animal studies is relatively limited. The COXPRESdb (http://coxpresdb.jp) provides coexpression relationships for multiple animal species, as comparisons of coexpressed gene lists can enhance the reliability of gene coexpression determinations. Here, we report the updates of the database, mainly focusing on the following two points. First, we updated our coexpression data by including recent microarray data for the previous seven species (human, mouse, rat, chicken, fly, zebrafish and nematode) and adding four new species (monkey, dog, budding yeast and fission yeast), along with a new human microarray platform. A reliability scoring function was also implemented, based on coexpression conservation to filter out coexpression with low reliability. Second, the network drawing function was updated, to implement automatic cluster analyses with enrichment analyses in Gene Ontology and in cis elements, along with interactive network analyses with Cytoscape Web. With these updates, COXPRESdb will become a more powerful tool for analyses of functional and regulatory networks of genes in a variety of animal species. Oxford University Press 2013-01 2012-11-29 /pmc/articles/PMC3531062/ /pubmed/23203868 http://dx.doi.org/10.1093/nar/gks1014 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com.
spellingShingle Articles
Obayashi, Takeshi
Okamura, Yasunobu
Ito, Satoshi
Tadaka, Shu
Motoike, Ikuko N.
Kinoshita, Kengo
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
title COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
title_full COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
title_fullStr COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
title_full_unstemmed COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
title_short COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals
title_sort coxpresdb: a database of comparative gene coexpression networks of eleven species for mammals
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531062/
https://www.ncbi.nlm.nih.gov/pubmed/23203868
http://dx.doi.org/10.1093/nar/gks1014
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