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Although this plasticity has been extensively studied in the model cyanobacterium <jats:italic>Synechocystis<\/jats:italic> sp. PCC 6803, a detailed analysis of the coordinated transcriptional adaption across varying conditions is lacking. Here, we report a meta-analysis of 756 individual microarray measurements conducted in 37 independent studies-the most comprehensive study of the <jats:italic>Synechocystis<\/jats:italic> transcriptome to date. Using stringent statistical evaluation, we characterized the coordinated adaptation of <jats:italic>Synechocystis<\/jats:italic>\u2019 gene expression on systems level. Evaluation of the data revealed that the photosynthetic apparatus is subjected to greater changes in expression than other cellular components. Nevertheless, network analyses indicated a significant degree of transcriptional coordination of photosynthesis and various metabolic processes, and revealed the tight co-regulation of components of photosystems I, II and phycobilisomes. Detailed inspection of the integrated data led to the discovery a variety of regulatory patterns and novel putative photosynthetic genes. Intriguingly, global clustering analyses suggested contrasting transcriptional response of metabolic and regulatory genes stress to conditions. The integrated <jats:italic>Synechocystis<\/jats:italic> transcriptome can be accessed and interactively analyzed via the CyanoEXpress website (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/cyanoexpress.sysbiolab.eu\">http:\/\/cyanoexpress.sysbiolab.eu<\/jats:ext-link>).<\/jats:p>","DOI":"10.1038\/srep22168","type":"journal-article","created":{"date-parts":[[2016,2,29]],"date-time":"2016-02-29T12:54:44Z","timestamp":1456750484000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":42,"title":["The Transcriptional Landscape of the Photosynthetic Model Cyanobacterium Synechocystis sp. PCC6803"],"prefix":"10.1038","volume":"6","author":[{"given":"Miguel A.","family":"Hern\u00e1ndez-Prieto","sequence":"first","affiliation":[]},{"given":"Trudi Ann","family":"Semeniuk","sequence":"additional","affiliation":[]},{"given":"Joaqu\u00edn","family":"Giner-Lamia","sequence":"additional","affiliation":[]},{"given":"Matthias E.","family":"Futschik","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2016,2,29]]},"reference":[{"key":"BFsrep22168_CR1","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1038\/nature07381","volume":"455","author":"B Rasmussen","year":"2008","unstructured":"Rasmussen, B., Fletcher, I. R., Brocks, J. J. & Kilburn, M. R. Reassessing the first appearance of eukaryotes and cyanobacteria. 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