Validating regulatory predictions from diverse bacteria with mutant fitness data
Publication Date
May 24, 2017
Authors
Shiori Sagawa, Morgan N. Price, Adam M. Deutschbauer & Adam P. Arkin
Volume
12
Issue
5
Pages
e0178258
DOI
https://dx.plos.org/10.1371/journal.pone.0178258
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0178258
Scopus
85019872465
Mendeley
http://www.mendeley.com/research/validating-regulatory-predictions-diverse-bacteria-mutant-fitness-data
Events
Loading … Spinner

Mendeley | Further Information

{"title"=>"Validating regulatory predictions from diverse bacteria with mutant fitness data", "type"=>"journal", "authors"=>[{"first_name"=>"Shiori", "last_name"=>"Sagawa", "scopus_author_id"=>"56311111300"}, {"first_name"=>"Morgan N.", "last_name"=>"Price", "scopus_author_id"=>"8849984000"}, {"first_name"=>"Adam M.", "last_name"=>"Deutschbauer", "scopus_author_id"=>"6507191963"}, {"first_name"=>"Adam P.", "last_name"=>"Arkin", "scopus_author_id"=>"7006902792"}], "year"=>2017, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-85019872465", "sgr"=>"85019872465", "pui"=>"616339980", "isbn"=>"1111111111", "pmid"=>"28542589", "doi"=>"10.1371/journal.pone.0178258"}, "id"=>"5f7273c7-d8f6-3322-949e-b333a5cbbca2", "abstract"=>"Although transcriptional regulation is fundamental to understanding bacterial physiology, the targets of most bacterial transcription factors are not known. Comparative genomics has been used to identify likely targets of some of these transcription factors, but these predictions typically lack experimental support. Here, we used mutant fitness data, which measures the importance of each gene for a bacterium’s growth across many conditions, to test regulatory predictions from RegPrecise, a curated collection of comparative genomics predictions. Because characterized transcription factors often have correlated fitness with one of their targets (either positively or negatively), correlated fitness patterns provide support for the comparative genomics predictions. At a false discovery rate of 3%, we identified significant cofitness for at least one target of 158 TFs in 107 ortholog groups and from 24 bacteria. Thus, high-throughput genetics can be used to identify a high-confidence subset of the sequence-based regulatory predictions.", "link"=>"http://www.mendeley.com/research/validating-regulatory-predictions-diverse-bacteria-mutant-fitness-data", "reader_count"=>10, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>5, "Student > Postgraduate"=>1, "Other"=>1, "Student > Bachelor"=>1, "Student > Ph. D. Student"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>5, "Student > Postgraduate"=>1, "Other"=>1, "Student > Bachelor"=>1, "Student > Ph. D. Student"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>4}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>2}, "group_count"=>0}

Scopus | Further Information

{"@_fa"=>"true", "link"=>[{"@_fa"=>"true", "@ref"=>"self", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85019872465"}, {"@_fa"=>"true", "@ref"=>"author-affiliation", "@href"=>"https://api.elsevier.com/content/abstract/scopus_id/85019872465?field=author,affiliation"}, {"@_fa"=>"true", "@ref"=>"scopus", "@href"=>"https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85019872465&origin=inward"}, {"@_fa"=>"true", "@ref"=>"scopus-citedby", "@href"=>"https://www.scopus.com/inward/citedby.uri?partnerID=HzOxMe3b&scp=85019872465&origin=inward"}], "prism:url"=>"https://api.elsevier.com/content/abstract/scopus_id/85019872465", "dc:identifier"=>"SCOPUS_ID:85019872465", "eid"=>"2-s2.0-85019872465", "dc:title"=>"Validating regulatory predictions from diverse bacteria with mutant fitness data", "dc:creator"=>"Sagawa S.", "prism:publicationName"=>"PLoS ONE", "prism:eIssn"=>"19326203", "prism:volume"=>"12", "prism:issueIdentifier"=>"5", "prism:pageRange"=>nil, "prism:coverDate"=>"2017-05-01", "prism:coverDisplayDate"=>"May 2017", "prism:doi"=>"10.1371/journal.pone.0178258", "citedby-count"=>"5", "affiliation"=>[{"@_fa"=>"true", "affilname"=>"University of California, Berkeley", "affiliation-city"=>"Berkeley", "affiliation-country"=>"United States"}, {"@_fa"=>"true", "affilname"=>"Lawrence Berkeley National Laboratory", "affiliation-city"=>"Berkeley", "affiliation-country"=>"United States"}], "pubmed-id"=>"28542589", "prism:aggregationType"=>"Journal", "subtype"=>"ar", "subtypeDescription"=>"Article", "article-number"=>"e0178258", "source-id"=>"10600153309", "openaccess"=>"1", "openaccessFlag"=>true}

Counter

  • {"month"=>"5", "year"=>"2017", "pdf_views"=>"33", "xml_views"=>"10", "html_views"=>"322"}
  • {"month"=>"6", "year"=>"2017", "pdf_views"=>"27", "xml_views"=>"3", "html_views"=>"85"}
  • {"month"=>"7", "year"=>"2017", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"64"}
  • {"month"=>"8", "year"=>"2017", "pdf_views"=>"22", "xml_views"=>"1", "html_views"=>"39"}
  • {"month"=>"9", "year"=>"2017", "pdf_views"=>"14", "xml_views"=>"1", "html_views"=>"35"}
  • {"month"=>"10", "year"=>"2017", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"62"}
  • {"month"=>"11", "year"=>"2017", "pdf_views"=>"1", "xml_views"=>"0", "html_views"=>"89"}
  • {"month"=>"12", "year"=>"2017", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"170"}
  • {"month"=>"1", "year"=>"2018", "pdf_views"=>"9", "xml_views"=>"0", "html_views"=>"33"}
  • {"month"=>"2", "year"=>"2018", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"14"}
  • {"month"=>"3", "year"=>"2018", "pdf_views"=>"12", "xml_views"=>"0", "html_views"=>"28"}
  • {"month"=>"4", "year"=>"2018", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"11"}
  • {"month"=>"5", "year"=>"2018", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"8"}
  • {"month"=>"6", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"3", "html_views"=>"10"}
  • {"month"=>"7", "year"=>"2018", "pdf_views"=>"5", "xml_views"=>"3", "html_views"=>"7"}
  • {"month"=>"8", "year"=>"2018", "pdf_views"=>"0", "xml_views"=>"1", "html_views"=>"12"}
  • {"month"=>"9", "year"=>"2018", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"14"}
  • {"month"=>"10", "year"=>"2018", "pdf_views"=>"2", "xml_views"=>"1", "html_views"=>"12"}
  • {"month"=>"11", "year"=>"2018", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"13"}
  • {"month"=>"12", "year"=>"2018", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"16"}
  • {"month"=>"1", "year"=>"2019", "pdf_views"=>"3", "xml_views"=>"0", "html_views"=>"14"}
  • {"month"=>"2", "year"=>"2019", "pdf_views"=>"15", "xml_views"=>"0", "html_views"=>"11"}
  • {"month"=>"3", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"12"}
  • {"month"=>"4", "year"=>"2019", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"11"}
  • {"month"=>"5", "year"=>"2019", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"7"}
  • {"month"=>"6", "year"=>"2019", "pdf_views"=>"5", "xml_views"=>"0", "html_views"=>"11"}
  • {"month"=>"7", "year"=>"2019", "pdf_views"=>"12", "xml_views"=>"4", "html_views"=>"4"}
  • {"month"=>"8", "year"=>"2019", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"5"}
  • {"month"=>"9", "year"=>"2019", "pdf_views"=>"11", "xml_views"=>"0", "html_views"=>"8"}
  • {"month"=>"10", "year"=>"2019", "pdf_views"=>"13", "xml_views"=>"0", "html_views"=>"9"}
  • {"month"=>"11", "year"=>"2019", "pdf_views"=>"3", "xml_views"=>"2", "html_views"=>"5"}
  • {"month"=>"12", "year"=>"2019", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"3"}
  • {"month"=>"1", "year"=>"2020", "pdf_views"=>"12", "xml_views"=>"1", "html_views"=>"9"}
  • {"month"=>"2", "year"=>"2020", "pdf_views"=>"12", "xml_views"=>"1", "html_views"=>"6"}
  • {"month"=>"3", "year"=>"2020", "pdf_views"=>"8", "xml_views"=>"0", "html_views"=>"12"}
  • {"month"=>"4", "year"=>"2020", "pdf_views"=>"10", "xml_views"=>"0", "html_views"=>"8"}
  • {"month"=>"5", "year"=>"2020", "pdf_views"=>"9", "xml_views"=>"1", "html_views"=>"5"}
  • {"month"=>"6", "year"=>"2020", "pdf_views"=>"6", "xml_views"=>"1", "html_views"=>"1"}
  • {"month"=>"7", "year"=>"2020", "pdf_views"=>"4", "xml_views"=>"0", "html_views"=>"3"}
  • {"month"=>"8", "year"=>"2020", "pdf_views"=>"7", "xml_views"=>"0", "html_views"=>"0"}
  • {"month"=>"9", "year"=>"2020", "pdf_views"=>"2", "xml_views"=>"0", "html_views"=>"1"}

PMC Usage Stats

  • {"unique-ip"=>"13", "full-text"=>"14", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"6"}
  • {"unique-ip"=>"15", "full-text"=>"15", "pdf"=>"5", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"7"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2017", "month"=>"8"}
  • {"unique-ip"=>"16", "full-text"=>"15", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"6", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"9"}
  • {"unique-ip"=>"9", "full-text"=>"8", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"10"}
  • {"unique-ip"=>"9", "full-text"=>"7", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2017", "month"=>"11"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"5", "full-text"=>"6", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"1"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"11"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"9"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"7", "full-text"=>"4", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"4"}
  • {"unique-ip"=>"8", "full-text"=>"7", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"6"}
  • {"unique-ip"=>"7", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"5", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"10"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"8", "full-text"=>"8", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"10", "full-text"=>"6", "pdf"=>"7", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"10"}
  • {"unique-ip"=>"1", "full-text"=>"0", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}
  • {"unique-ip"=>"4", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"2"}
  • {"unique-ip"=>"4", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"3"}
  • {"unique-ip"=>"7", "full-text"=>"4", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"4", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"4"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"5"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"6"}
  • {"unique-ip"=>"6", "full-text"=>"5", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"3", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
Loading … Spinner
There are currently no alerts