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This study integrates genetic, genomic and systems approaches to identify a genetically perturbed gene network that is regulated by the interaction of carbon and light signaling in Arabidopsis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p><jats:underline>C<\/jats:underline>arbon and<jats:underline>l<\/jats:underline>ight<jats:underline>i<\/jats:underline>nsensitive (<jats:italic>cli<\/jats:italic>) mutants were isolated. Microarray data from<jats:italic>cli186<\/jats:italic>is analyzed to identify the genes, biological processes and gene networks affected by the integration of light and carbon pathways. Analysis of this data reveals 966 genes regulated by light and\/or carbon signaling in wild-type. In<jats:italic>cli186<\/jats:italic>, 216 of these light\/carbon regulated genes are misregulated in response to light and\/or carbon treatments where 78% are misregulated in response to light and carbon interactions. Analysis of the gene lists show that genes in the biological processes \"energy\" and \"metabolism\" are over-represented among the 966 genes regulated by carbon and\/or light in wild-type, and the 216 misregulated genes in<jats:italic>cli186<\/jats:italic>. To understand connections among carbon and\/or light regulated genes in wild-type and the misregulated genes in<jats:italic>cli186<\/jats:italic>, the microarray data is interpreted in the context of metabolic and regulatory networks. The network created from the 966 light\/carbon regulated genes in wild-type, reveals that<jats:italic>cli186<\/jats:italic>is affected in the light and\/or carbon regulation of a network of 60 connected genes, including six transcription factors. One transcription factor, HAT22 appears to be a regulatory \"hub\" in the<jats:italic>cli186<\/jats:italic>network as it shows regulatory connections linking a metabolic network of genes involved in \"amino acid metabolism\", \"C-compound\/carbohydrate metabolism\" and \"glycolysis\/gluconeogenesis\".<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The global misregulation of gene networks controlled by light and carbon signaling in<jats:italic>cli186<\/jats:italic>indicates that it represents one of the first Arabidopsis mutants isolated that is specifically disrupted in the integration of both carbon and light signals to control the regulation of metabolic, developmental and regulatory genes. The network analysis of misregulated genes suggests that<jats:italic>CLI186<\/jats:italic>acts to integrate light and carbon signaling interactions and is a master regulator connecting the regulation of a host of downstream metabolic and regulatory processes.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1752-0509-2-31","type":"journal-article","created":{"date-parts":[[2008,4,4]],"date-time":"2008-04-04T06:13:25Z","timestamp":1207289605000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":49,"title":["An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis"],"prefix":"10.1186","volume":"2","author":[{"given":"Karen E","family":"Thum","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael J","family":"Shin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodrigo A","family":"Guti\u00e9rrez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Indrani","family":"Mukherjee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manpreet S","family":"Katari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damion","family":"Nero","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dennis","family":"Shasha","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gloria M","family":"Coruzzi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,4,4]]},"reference":[{"key":"188_CR1","first-page":"203","volume":"13","author":"C Fankhauser","year":"1997","unstructured":"Fankhauser C, Chory J: Light control of plant development. 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