{"id":"https://openalex.org/W2156559501","doi":"https://doi.org/10.1186/1471-2105-7-505","title":"Using local gene expression similarities to discover regulatory binding site modules","display_name":"Using local gene expression similarities to discover regulatory binding site modules","publication_year":2006,"publication_date":"2006-11-17","ids":{"openalex":"https://openalex.org/W2156559501","doi":"https://doi.org/10.1186/1471-2105-7-505","mag":"2156559501","pmid":"https://pubmed.ncbi.nlm.nih.gov/17109764"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-505","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-505","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-505","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/10.1186/1471-2105-7-505","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081814379","display_name":"Bartek Wilczy\u0144ski","orcid":"https://orcid.org/0000-0002-8134-0589"},"institutions":[{"id":"https://openalex.org/I99542240","display_name":"Polish Academy of Sciences","ror":"https://ror.org/01dr6c206","country_code":"PL","type":"government","lineage":["https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Bartek Wilczy\u0144ski","raw_affiliation_strings":["lnstitute of Mathematics, Polish Academy of Sciences, Warsaw, Poland. bartek@impan.gov.pl <bartek@impan.gov.pl>","lnstitute of Mathematics, Polish Academy of Sciences, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"lnstitute of Mathematics, Polish Academy of Sciences, Warsaw, Poland. bartek@impan.gov.pl <bartek@impan.gov.pl>","institution_ids":["https://openalex.org/I99542240"]},{"raw_affiliation_string":"lnstitute of Mathematics, Polish Academy of Sciences, Warsaw, Poland","institution_ids":["https://openalex.org/I99542240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022568938","display_name":"Torgeir R. Hvidsten","orcid":"https://orcid.org/0000-0001-6097-2539"},"institutions":[{"id":"https://openalex.org/I223464139","display_name":"Linnaeus University","ror":"https://ror.org/00j9qag85","country_code":"SE","type":"education","lineage":["https://openalex.org/I223464139"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Torgeir R Hvidsten","raw_affiliation_strings":["Linnaeus Centre for Bioinformatics, Uppsala, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Linnaeus Centre for Bioinformatics, Uppsala, Sweden","institution_ids":["https://openalex.org/I223464139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046112262","display_name":"Andriy Kryshtafovych","orcid":"https://orcid.org/0000-0001-5066-7178"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andriy Kryshtafovych","raw_affiliation_strings":["Genome Center, UC Davis, Davis, CA, USA","Genome Center, UC Davis, Davis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Center, UC Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Genome Center, UC Davis, Davis, USA","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023573472","display_name":"Jerzy Tiuryn","orcid":"https://orcid.org/0000-0002-0285-5606"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Jerzy Tiuryn","raw_affiliation_strings":["Institute of Informatics, Warsaw University, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics, Warsaw University, Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050406527","display_name":"Jan Komorowski","orcid":"https://orcid.org/0000-0002-0766-8789"},"institutions":[{"id":"https://openalex.org/I223464139","display_name":"Linnaeus University","ror":"https://ror.org/00j9qag85","country_code":"SE","type":"education","lineage":["https://openalex.org/I223464139"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Jan Komorowski","raw_affiliation_strings":["Linnaeus Centre for Bioinformatics, Uppsala, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Linnaeus Centre for Bioinformatics, Uppsala, Sweden","institution_ids":["https://openalex.org/I223464139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074974770","display_name":"Krzysztof Fidelis","orcid":"https://orcid.org/0000-0002-8061-412X"},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Krzysztof Fidelis","raw_affiliation_strings":["Genome Center, UC Davis, Davis, CA, USA","Genome Center, UC Davis, Davis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome Center, UC Davis, Davis, CA, USA","institution_ids":["https://openalex.org/I84218800"]},{"raw_affiliation_string":"Genome Center, UC Davis, Davis, USA","institution_ids":["https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074974770"],"corresponding_institution_ids":["https://openalex.org/I84218800"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.0174,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.74150497,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"7","issue":"1","first_page":"505","last_page":"505"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8210999965667725,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8210999965667725,"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/T10885","display_name":"Gene expression and cancer classification","score":0.07660000026226044,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.043800000101327896,"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/dna-microarray","display_name":"DNA microarray","score":0.6550155878067017},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.597924530506134},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5775874853134155},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5402036309242249},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5103766322135925},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5065933465957642},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4856347143650055},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4532542824745178},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.42996177077293396},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.42350855469703674},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.41217243671417236},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3701164722442627},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3588055968284607},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.2772975265979767},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.259141206741333}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6550155878067017},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.597924530506134},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5775874853134155},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5402036309242249},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5103766322135925},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5065933465957642},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4856347143650055},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4532542824745178},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.42996177077293396},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.42350855469703674},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.41217243671417236},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3701164722442627},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3588055968284607},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.2772975265979767},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.259141206741333},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005656","descriptor_name":"Fungal Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005810","descriptor_name":"Multigene Family","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-7-505","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-505","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-505","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:17109764","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17109764","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:pubmedcentral.nih.gov:2001304","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2001304","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"},{"id":"pmh:oai:doaj.org/article:d99641ac051f483ea776fa0d901dea96","is_oa":false,"landing_page_url":"https://doaj.org/article/d99641ac051f483ea776fa0d901dea96","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 7, Iss 1, p 505 (2006)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-505","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-505","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-505","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":[],"funders":[{"id":"https://openalex.org/F4320320940","display_name":"Stiftelsen f\u00f6r\u00a0Strategisk Forskning","ror":"https://ror.org/044wr7g58"},{"id":"https://openalex.org/F4320322327","display_name":"Knut och Alice Wallenbergs Stiftelse","ror":"https://ror.org/004hzzk67"},{"id":"https://openalex.org/F4320338286","display_name":"Lawrence Livermore National Laboratory","ror":"https://ror.org/041nk4h53"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2156559501.pdf","grobid_xml":"https://content.openalex.org/works/W2156559501.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1483505747","https://openalex.org/W1493217831","https://openalex.org/W1557923305","https://openalex.org/W1575009136","https://openalex.org/W1586476557","https://openalex.org/W1592870802","https://openalex.org/W1970074386","https://openalex.org/W1989373239","https://openalex.org/W2003967338","https://openalex.org/W2005652623","https://openalex.org/W2037940015","https://openalex.org/W2073727170","https://openalex.org/W2080498142","https://openalex.org/W2084908610","https://openalex.org/W2096280725","https://openalex.org/W2100471807","https://openalex.org/W2103017472","https://openalex.org/W2103325210","https://openalex.org/W2108420379","https://openalex.org/W2109619915","https://openalex.org/W2115761267","https://openalex.org/W2125508747","https://openalex.org/W2126602684","https://openalex.org/W2128091972","https://openalex.org/W2128936012","https://openalex.org/W2135230352","https://openalex.org/W2136549265","https://openalex.org/W2137970956","https://openalex.org/W2141408320","https://openalex.org/W2142460132","https://openalex.org/W2153978438","https://openalex.org/W2166898290","https://openalex.org/W2167190345","https://openalex.org/W2168157737","https://openalex.org/W2170778160","https://openalex.org/W4210774122","https://openalex.org/W4211024376","https://openalex.org/W4232953319","https://openalex.org/W4239029175","https://openalex.org/W4255833381"],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W2392243736","https://openalex.org/W86652014","https://openalex.org/W2375480909","https://openalex.org/W2353314428","https://openalex.org/W4321636575","https://openalex.org/W2357796999","https://openalex.org/W2045526782","https://openalex.org/W2381031055","https://openalex.org/W2366070815"],"abstract_inverted_index":{"BACKGROUND:":[0],"We":[1,65,81],"present":[2],"an":[3,59],"approach":[4,190],"designed":[5],"to":[6,24,35,44,73,140,226],"identify":[7],"gene":[8,42],"regulation":[9],"patterns":[10],"using":[11],"sequence":[12,215],"and":[13,58,87,134,183,216],"expression":[14,46,55,78,117,162,217],"data":[15,118,133],"collected":[16],"for":[17],"Saccharomyces":[18],"cerevisae.":[19,97],"Our":[20,189],"main":[21],"goal":[22],"is":[23,208],"relate":[25],"the":[26,45,84,107,112,170,206],"combinations":[27],"of":[28,47,70,102,106,109,122,169,176,178,205],"transcription":[29],"factor":[30],"binding":[31,37,187],"sites":[32],"(also":[33],"referred":[34],"as":[36],"site":[38],"modules)":[39],"identified":[40],"in":[41,174],"promoters":[43],"these":[48,142],"genes.":[49,124],"The":[50,98,219],"novel":[51],"aspects":[52],"include":[53,74],"local":[54,161],"similarity":[56,163],"clustering":[57,164],"exact":[60],"IF-THEN":[61],"rule":[62,71],"inference":[63],"algorithm.":[64],"also":[66],"provide":[67],"a":[68],"method":[69,207],"generalization":[72],"genes":[75,110],"with":[76,150,185],"unknown":[77],"profiles.":[79],"RESULTS:":[80],"have":[82,129],"implemented":[83],"proposed":[85],"framework":[86],"tested":[88],"it":[89],"on":[90,195,212],"publicly":[91],"available":[92],"datasets":[93],"from":[94,116],"yeast":[95],"S.":[96],"testing":[99],"procedure":[100,221],"consists":[101],"thorough":[103],"statistical":[104],"analyses":[105],"groups":[108],"matching":[111],"rules":[113],"we":[114,128,146,157],"infer":[115],"against":[119],"known":[120],"sets":[121],"co-regulated":[123],"For":[125],"this":[126],"purpose":[127],"used":[130],"published":[131,152],"ChIP-Chip":[132,186],"Gene":[135,179],"Ontology":[136,180],"annotations.":[137],"In":[138],"order":[139],"make":[141],"tests":[143],"more":[144],"objective":[145],"compare":[147],"our":[148],"results":[149],"recently":[151],"similar":[153],"studies.":[154],"CONCLUSION:":[155],"Results":[156],"obtain":[158],"show":[159],"that":[160,197],"greatly":[165],"enhances":[166],"overall":[167],"quality":[168],"derived":[171],"rules,":[172],"both":[173],"terms":[175],"enrichment":[177],"functional":[181],"annotation":[182],"coherence":[184],"data.":[188,218],"thus":[191],"provides":[192],"reliable":[193],"hypotheses":[194],"co-regulation":[196],"can":[198,222],"be":[199,223],"experimentally":[200],"verified.":[201],"An":[202],"important":[203],"feature":[204],"its":[209],"reliance":[210],"only":[211],"widely":[213],"accessible":[214],"same":[220],"easily":[224],"applied":[225],"other":[227],"microbial":[228],"organisms.":[229]},"counts_by_year":[{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}