Synergy: A Web Resource for Exploring Gene Regulation in Synechocystis sp. PCC6803
- Publication Date
- November 24, 2014
- Journal
- PLOS ONE
- Authors
- Niklas Mähler, Otilia Cheregi, Christiane Funk, Sergiu Netotea, et al
- Volume
- 9
- Issue
- 11
- Pages
- e113496
- DOI
- https://dx.plos.org/10.1371/journal.pone.0113496
- Publisher URL
- http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0113496
- PubMed
- http://www.ncbi.nlm.nih.gov/pubmed/25420108
- PubMed Central
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4242644
- Europe PMC
- http://europepmc.org/abstract/MED/25420108
- Web of Science
- 000346766900041
- Scopus
- 84912535178
- Mendeley
- http://www.mendeley.com/research/synergy-web-resource-exploring-gene-regulation-synechocystis-sp-pcc6803
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Mendeley | Further Information
{"title"=>"Synergy: A web resource for exploring gene regulation in Synechocystis sp. PCC6803", "type"=>"journal", "authors"=>[{"first_name"=>"Niklas", "last_name"=>"Mähler", "scopus_author_id"=>"56431028700"}, {"first_name"=>"Otilia", "last_name"=>"Cheregi", "scopus_author_id"=>"8837079900"}, {"first_name"=>"Christiane", "last_name"=>"Funk", "scopus_author_id"=>"7102175069"}, {"first_name"=>"Sergiu", "last_name"=>"Netotea", "scopus_author_id"=>"16307931700"}, {"first_name"=>"Torgeir R.", "last_name"=>"Hvidsten", "scopus_author_id"=>"6506415063"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"600596277", "scopus"=>"2-s2.0-84912535178", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"25420108", "sgr"=>"84912535178", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0113496"}, "id"=>"efa5d09b-beae-3c13-b9c1-be801d1afe9d", "abstract"=>"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.", "link"=>"http://www.mendeley.com/research/synergy-web-resource-exploring-gene-regulation-synechocystis-sp-pcc6803", "reader_count"=>23, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>7, "Student > Master"=>4, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>8, "Student > Ph. D. Student"=>7, "Student > Master"=>4, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Environmental Science"=>3, "Biochemistry, Genetics and Molecular Biology"=>3, "Medicine and Dentistry"=>1, "Agricultural and Biological Sciences"=>12, "Chemistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>12}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>3}}, "reader_count_by_country"=>{"Norway"=>2}, "group_count"=>1}Scopus | Further Information
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Relative Metric
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