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Synergy: a web resource for exploring gene regulation in Synechocystis sp. PCC6803
Umeå University, Faculty of Science and Technology, Department of Chemistry.
Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
Umeå University, Faculty of Science and Technology, Department of Chemistry. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC). Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Computational Life Science Cluster, Umeå University, Umeå, Sweden.
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2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 11, e113496Article in journal (Refereed) Published
Abstract [en]

Despite being a highly studied model organism, most genes of the cyanobacterium Synechocystis sp. PCC 6803 encode proteins with completely unknown function. To facilitate studies of gene regulation in Synechocystis, we have developed Synergy (http://synergy.plantgenie.org), a web application integrating co-expression networks and regulatory motif analysis. Co-expression networks were inferred from publicly available microarray experiments, while regulatory motifs were identified using a phylogenetic footprinting approach. Automatically discovered motifs were shown to be enriched in the network neighborhoods of regulatory proteins much more often than in the neighborhoods of non-regulatory genes, showing that the data provide a sound starting point for studying gene regulation in Synechocystis. Concordantly, we provide several case studies demonstrating that Synergy can be used to find biologically relevant regulatory mechanisms in Synechocystis. Synergy can be used to interactively perform analyses such as gene/motif search, network visualization and motif/function enrichment. Considering the importance of Synechocystis for photosynthesis and biofuel research, we believe that Synergy will become a valuable resource to the research community.

Place, publisher, year, edition, pages
2014. Vol. 9, no 11, e113496
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Chemical Sciences Biological Sciences
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URN: urn:nbn:se:umu:diva-100364DOI: 10.1371/journal.pone.0113496ISI: 000346766900041PubMedID: 25420108OAI: oai:DiVA.org:umu-100364DiVA: diva2:791764
Available from: 2015-03-02 Created: 2015-03-02 Last updated: 2017-12-04Bibliographically approved

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Cheregi, OtiliaFunk, ChristianeNetotea, Sergiu
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