{"id":"https://openalex.org/W1989594722","doi":"https://doi.org/10.1186/1471-2105-10-435","title":"In Silico Evaluation of Predicted Regulatory Interactions in Arabidopsis thaliana","display_name":"In Silico Evaluation of Predicted Regulatory Interactions in Arabidopsis thaliana","publication_year":2009,"publication_date":"2009-12-01","ids":{"openalex":"https://openalex.org/W1989594722","doi":"https://doi.org/10.1186/1471-2105-10-435","mag":"1989594722","pmid":"https://pubmed.ncbi.nlm.nih.gov/20025756"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-435","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-435","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-435","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-435","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076168564","display_name":"Damion Nero","orcid":null},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Damion Nero","raw_affiliation_strings":["Department of Biology, New York University, Center for Genomics and Systems Biology, New York, NY 10003, USA. dcn208@nyu.edu","Center for Genomics and Systems Biology, Department of Biology, New York University., New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, New York University, Center for Genomics and Systems Biology, New York, NY 10003, USA. dcn208@nyu.edu","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Center for Genomics and Systems Biology, Department of Biology, New York University., New York, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039310159","display_name":"Manpreet S. Katari","orcid":"https://orcid.org/0000-0002-3377-063X"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manpreet S Katari","raw_affiliation_strings":["Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY, 10003, USA","Center for Genomics and Systems Biology, Department of Biology, New York University., New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY, 10003, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Center for Genomics and Systems Biology, Department of Biology, New York University., New York, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014761635","display_name":"Jonathan Kelfer","orcid":null},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Kelfer","raw_affiliation_strings":["Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY, 10003, USA","Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA","Courant Institute of Mathematical Sciences, New York University, New York, USA","Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY, 10003, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, New York University, New York, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA","institution_ids":["https://openalex.org/I57206974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033150336","display_name":"Daniel Tranchina","orcid":"https://orcid.org/0000-0002-0439-8349"},"institutions":[{"id":"https://openalex.org/I36672615","display_name":"Courant Institute of Mathematical Sciences","ror":"https://ror.org/037tm7f56","country_code":"US","type":"education","lineage":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Tranchina","raw_affiliation_strings":["Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY, 10003, USA","Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA","Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA","Courant Institute of Mathematical Sciences, New York University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY, 10003, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, New York University, New York, NY, 10003, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]},{"raw_affiliation_string":"Center for Genomics and Systems Biology, Department of Biology, New York University, New York, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Courant Institute of Mathematical Sciences, New York University, New York, USA","institution_ids":["https://openalex.org/I36672615","https://openalex.org/I57206974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025597505","display_name":"Gloria M. Coruzzi","orcid":"https://orcid.org/0000-0003-2608-2166"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gloria M Coruzzi","raw_affiliation_strings":["Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY, 10003, USA","Center for Genomics and Systems Biology, Department of Biology, New York University., New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Genomics and Systems Biology, Department of Biology, New York University, 100 Washington Square East, 1009 Main Building, New York, NY, 10003, USA","institution_ids":["https://openalex.org/I57206974"]},{"raw_affiliation_string":"Center for Genomics and Systems Biology, Department of Biology, New York University., New York, USA","institution_ids":["https://openalex.org/I57206974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5076168564"],"corresponding_institution_ids":["https://openalex.org/I57206974"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1369,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.53368741,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"10","issue":"1","first_page":"435","last_page":"435"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.3610000014305115,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.3610000014305115,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.3228999972343445,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.12399999797344208,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6883178353309631},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.6464680433273315},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6419882774353027},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5581117868423462},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.5453824400901794},{"id":"https://openalex.org/keywords/spearmans-rank-correlation-coefficient","display_name":"Spearman's rank correlation coefficient","score":0.5104824304580688},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4539288878440857},{"id":"https://openalex.org/keywords/arabidopsis","display_name":"Arabidopsis","score":0.44525980949401855},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.4338521659374237},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.41495025157928467},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.41353243589401245},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.29635071754455566},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.23354071378707886},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14387983083724976},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.10590511560440063}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6883178353309631},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6464680433273315},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6419882774353027},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5581117868423462},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.5453824400901794},{"id":"https://openalex.org/C159744936","wikidata":"https://www.wikidata.org/wiki/Q1126730","display_name":"Spearman's rank correlation coefficient","level":2,"score":0.5104824304580688},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4539288878440857},{"id":"https://openalex.org/C2779491563","wikidata":"https://www.wikidata.org/wiki/Q157892","display_name":"Arabidopsis","level":4,"score":0.44525980949401855},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.4338521659374237},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.41495025157928467},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.41353243589401245},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.29635071754455566},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.23354071378707886},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14387983083724976},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.10590511560440063},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029681","descriptor_name":"Arabidopsis Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-10-435","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-435","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-435","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20025756","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20025756","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:696bd3a04001497fbe6ad5d6dcae7c84","is_oa":false,"landing_page_url":"https://doaj.org/article/696bd3a04001497fbe6ad5d6dcae7c84","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 10, Iss 1, p 435 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2803859","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2803859","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-435","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-435","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-435","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G124720195","display_name":"Conceptual Data Integration for the VirtualPlant","funder_award_id":"0445666","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2336969013","display_name":"Arabidopsis 2010: Nitrogen Networks in Plants","funder_award_id":"0519985","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4528233393","display_name":null,"funder_award_id":"GM032877","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1989594722.pdf","grobid_xml":"https://content.openalex.org/works/W1989594722.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1481395979","https://openalex.org/W1538931504","https://openalex.org/W1592870802","https://openalex.org/W1964895626","https://openalex.org/W1966181675","https://openalex.org/W1990187840","https://openalex.org/W1995963967","https://openalex.org/W1996936761","https://openalex.org/W2022326657","https://openalex.org/W2029057282","https://openalex.org/W2047708521","https://openalex.org/W2053288464","https://openalex.org/W2053884941","https://openalex.org/W2055237228","https://openalex.org/W2063705471","https://openalex.org/W2065716803","https://openalex.org/W2072152345","https://openalex.org/W2077116812","https://openalex.org/W2079567028","https://openalex.org/W2080498142","https://openalex.org/W2087680290","https://openalex.org/W2096879509","https://openalex.org/W2104171413","https://openalex.org/W2114373433","https://openalex.org/W2121995533","https://openalex.org/W2126052291","https://openalex.org/W2128667600","https://openalex.org/W2128901331","https://openalex.org/W2132139487","https://openalex.org/W2134515324","https://openalex.org/W2135655483","https://openalex.org/W2135961634","https://openalex.org/W2136067601","https://openalex.org/W2141119750","https://openalex.org/W2146872370","https://openalex.org/W2147848023","https://openalex.org/W2148944713","https://openalex.org/W2151155706","https://openalex.org/W2152135698","https://openalex.org/W2153522847","https://openalex.org/W2159675211","https://openalex.org/W2160631767","https://openalex.org/W2162441687","https://openalex.org/W2168179004","https://openalex.org/W2171713538","https://openalex.org/W2963964759","https://openalex.org/W4231132933","https://openalex.org/W4247674247"],"related_works":["https://openalex.org/W2041540252","https://openalex.org/W2796636403","https://openalex.org/W2415545834","https://openalex.org/W1547158732","https://openalex.org/W3203113381","https://openalex.org/W170658859","https://openalex.org/W1483316219","https://openalex.org/W4310366902","https://openalex.org/W3023720143","https://openalex.org/W2490137852"],"abstract_inverted_index":{"BACKGROUND:":[0],"Prediction":[1],"of":[2,15,38,125,148,153,221,235],"transcriptional":[3,292],"regulatory":[4,141,146,293],"mechanisms":[5,294],"in":[6,31,49,84,89,130,173,257,290,312],"Arabidopsis":[7],"has":[8,67],"become":[9],"increasingly":[10],"critical":[11],"with":[12,210,269,309],"the":[13,133,145,179,200,233,248,260],"explosion":[14],"genomic":[16],"data":[17,162,181,206,212,297,303],"now":[18],"available":[19],"for":[20,52,56,139,163,287],"both":[21],"gene":[22,25],"expression":[23,161],"and":[24,41,108,112,170,228,232,239,251,265,285],"sequence":[26,314],"composition.":[27],"We":[28,98],"have":[29],"shown":[30],"previous":[32],"work":[33],"1,":[34],"that":[35,165,247,298,304],"a":[36,94,149],"combination":[37,85,131,220],"correlation":[39,75,106,253,266],"measurements":[40],"cis-regulatory":[42,113],"element":[43,114],"(CRE)":[44,115],"detection":[45,79,116,264,311],"methods":[46,80,127,158],"are":[47,86],"effective":[48,88,135],"predicting":[50,90,291],"targets":[51,147],"candidate":[53],"transcription":[54,150],"factors":[55],"specific":[57],"case":[58],"studies":[59],"which":[60,74,124],"were":[61,166,196,259],"validated.":[62],"However,":[63],"to":[64,73,122,159,198,271,274],"date":[65],"there":[66],"been":[68],"no":[69],"quantitative":[70],"assessment":[71],"as":[72],"measures":[76,138],"or":[77,83,119,129,191,219,256],"CRE":[78,118,120,250,263,310],"used":[81,102,187],"alone":[82,255],"most":[87,134,261],"TF-->target":[91,201],"relationships":[92],"on":[93,105,188],"genome-wide":[95],"scale.":[96],"RESULTS:":[97],"tested":[99],"several":[100],"widely":[101],"methods,":[103,222,267],"based":[104],"(Pearson":[107],"Spearman":[109,252],"Rank":[110],"correlation)":[111],"(>or=1":[117],"over-representation),":[121],"determine":[123],"these":[126,157],"individually":[128],"is":[132,305],"by":[136],"various":[137],"making":[140],"predictions.":[142],"To":[143],"predict":[144,276],"factor":[151],"(TF)":[152],"interest,":[154],"we":[155,195,223],"applied":[156],"microarray":[160,205,211,296,302],"genes":[164],"regulated":[167],"over":[168],"treatment":[169],"control":[171],"conditions":[172,186],"wild":[174],"type":[175],"(WT)":[176],"plants.":[177,215],"Because":[178],"chosen":[180],"sets":[182],"included":[183],"identical":[184],"experimental":[185],"TF":[189],"over-expressor":[190],"T-DNA":[192],"knockout":[193],"plants,":[194,209],"able":[197],"test":[199],"predictions":[202],"made":[203],"using":[204,295],"from":[207,213],"WT":[208],"mutant/transgenic":[214],"For":[216],"each":[217],"method,":[218],"computed":[224],"sensitivity,":[225],"specificity,":[226],"positive":[227,240],"negative":[229],"predictive":[230,241],"value":[231,242],"F-measure":[234],"balance":[236],"between":[237],"sensitivity":[238],"(precision).":[243],"This":[244],"analysis":[245],"revealed":[246],">or=1":[249],"(used":[254],"combination)":[258],"balanced":[262],"respectively":[268],"regard":[270],"their":[272],"power":[273],"accurately":[275],"regulatory-target":[277],"interactions.":[278],"CONCLUSION:":[279],"These":[280],"findings":[281],"provide":[282],"an":[283],"approach":[284],"guidance":[286],"researchers":[288],"interested":[289],"they":[299],"generate":[300],"(or":[301],"publically":[306],"available)":[307],"combined":[308],"promoter":[313],"data.":[315]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}