{"id":"https://openalex.org/W2160377419","doi":"https://doi.org/10.1093/bioinformatics/bti307","title":"A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas","display_name":"A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas","publication_year":2005,"publication_date":"2005-02-04","ids":{"openalex":"https://openalex.org/W2160377419","doi":"https://doi.org/10.1093/bioinformatics/bti307","mag":"2160377419","pmid":"https://pubmed.ncbi.nlm.nih.gov/15699025"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti307","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti307","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/1789/48972624/bioinformatics_21_9_1789.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/1789/48972624/bioinformatics_21_9_1789.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021609806","display_name":"M. S. Stepanova","orcid":"https://orcid.org/0000-0002-4069-2764"},"institutions":[{"id":"https://openalex.org/I4210148309","display_name":"Vavilov Institute of General Genetics","ror":"https://ror.org/05ermrg42","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210148309"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"M. Stepanova","raw_affiliation_strings":["Center for Biomedical Genomics and BioInformatics, Molecular and Microbiology Department, College of Arts and Sciences, George Mason University, Fairfax, VA 22031, USA","Vavilov Institute of General Genetics Gubkina str, 3, GSP-1, 111991, Moscow, Russia#TAB#"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Genomics and BioInformatics, Molecular and Microbiology Department, College of Arts and Sciences, George Mason University, Fairfax, VA 22031, USA","institution_ids":[]},{"raw_affiliation_string":"Vavilov Institute of General Genetics Gubkina str, 3, GSP-1, 111991, Moscow, Russia#TAB#","institution_ids":["https://openalex.org/I4210148309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058689591","display_name":"Tatiana Tiazhelova","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148309","display_name":"Vavilov Institute of General Genetics","ror":"https://ror.org/05ermrg42","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210129690","https://openalex.org/I4210148309"]}],"countries":["RU"],"is_corresponding":false,"raw_author_name":"T. Tiazhelova","raw_affiliation_strings":["Vavilov Institute of General Genetics Gubkina str, 3, GSP-1, 111991, Moscow, Russia#TAB#"],"affiliations":[{"raw_affiliation_string":"Vavilov Institute of General Genetics Gubkina str, 3, GSP-1, 111991, Moscow, Russia#TAB#","institution_ids":["https://openalex.org/I4210148309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052562207","display_name":"Mikhail Skoblov","orcid":"https://orcid.org/0000-0002-7293-3438"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"M. Skoblov","raw_affiliation_strings":["Center for Biomedical Genomics and BioInformatics, Molecular and Microbiology Department, College of Arts and Sciences, George Mason University, Fairfax, VA 22031, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Genomics and BioInformatics, Molecular and Microbiology Department, College of Arts and Sciences, George Mason University, Fairfax, VA 22031, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065986636","display_name":"Ancha Baranova","orcid":"https://orcid.org/0000-0001-6810-5982"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"A. Baranova","raw_affiliation_strings":["Center for Biomedical Genomics and BioInformatics, Molecular and Microbiology Department, College of Arts and Sciences, George Mason University, Fairfax, VA 22031, USA"],"affiliations":[{"raw_affiliation_string":"Center for Biomedical Genomics and BioInformatics, Molecular and Microbiology Department, College of Arts and Sciences, George Mason University, Fairfax, VA 22031, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5021609806"],"corresponding_institution_ids":["https://openalex.org/I4210148309"],"apc_list":null,"apc_paid":null,"fwci":1.2307,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.77927287,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"21","issue":"9","first_page":"1789","last_page":"1796"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987999796867371,"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/T12929","display_name":"Animal Genetics and Reproduction","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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-binding-site","display_name":"DNA binding site","score":0.760848879814148},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.645671010017395},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6359301805496216},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6046182513237},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5757352113723755},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5730277299880981},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.560314416885376},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5496323704719543},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.459824800491333},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4100266098976135},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17706283926963806}],"concepts":[{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.760848879814148},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.645671010017395},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6359301805496216},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6046182513237},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5757352113723755},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5730277299880981},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.560314416885376},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5496323704719543},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.459824800491333},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4100266098976135},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17706283926963806},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012689","descriptor_name":"Sequence Homology, Nucleic Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014714","descriptor_name":"Vertebrates","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti307","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti307","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/1789/48972624/bioinformatics_21_9_1789.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:15699025","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15699025","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti307","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti307","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/9/1789/48972624/bioinformatics_21_9_1789.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323155","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2160377419.pdf","grobid_xml":"https://content.openalex.org/works/W2160377419.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1500436854","https://openalex.org/W1653668857","https://openalex.org/W1971833582","https://openalex.org/W1983405741","https://openalex.org/W2013213258","https://openalex.org/W2021931962","https://openalex.org/W2046770376","https://openalex.org/W2063014741","https://openalex.org/W2064879068","https://openalex.org/W2072329780","https://openalex.org/W2087700126","https://openalex.org/W2087887622","https://openalex.org/W2097040991","https://openalex.org/W2101545714","https://openalex.org/W2112444654","https://openalex.org/W2126643821","https://openalex.org/W2130811773","https://openalex.org/W2133383018","https://openalex.org/W2134026743","https://openalex.org/W2151464048","https://openalex.org/W2168909179","https://openalex.org/W2340097947","https://openalex.org/W2559313591","https://openalex.org/W2799137445","https://openalex.org/W3106887353"],"related_works":["https://openalex.org/W1969771092","https://openalex.org/W2795723184","https://openalex.org/W2025529750","https://openalex.org/W2139566393","https://openalex.org/W2146517458","https://openalex.org/W2379997263","https://openalex.org/W2367493320","https://openalex.org/W2131580913","https://openalex.org/W3083097828","https://openalex.org/W2125854412"],"abstract_inverted_index":{"F-values":[0],"and":[1,12],"real":[2],"TFBS":[3],"occurrences":[4],"calculated":[5],"for":[6,17],"human,":[7],"chimp,":[8],"mouse,":[9],"rat,":[10],"zebrafish":[11],"fugu":[13],"genomes":[14],"are":[15],"available":[16],"free":[18],"download":[19],"at":[20],"http://www.gmu.edu/departments/mmb/baranova/pages/bioinformatics":[21]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}