{"id":"https://openalex.org/W2964526879","doi":"https://doi.org/10.1093/bioinformatics/btz573","title":"TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets","display_name":"TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets","publication_year":2019,"publication_date":"2019-07-24","ids":{"openalex":"https://openalex.org/W2964526879","doi":"https://doi.org/10.1093/bioinformatics/btz573","mag":"2964526879","pmid":"https://pubmed.ncbi.nlm.nih.gov/31347689"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5339/48978133/bioinformatics_35_24_5339.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5339/48978133/bioinformatics_35_24_5339.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055562731","display_name":"Laura Puente-Santamar\u00eda","orcid":"https://orcid.org/0000-0001-9034-4576"},"institutions":[{"id":"https://openalex.org/I4210091816","display_name":"Instituto de Investigaciones Biom\u00e9dicas Sols-Morreale","ror":"https://ror.org/00ha1f767","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210091816","https://openalex.org/I63634437"]},{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Laura Puente-Santamaria","raw_affiliation_strings":["Departamento de Bioqu\u00edmica, Universidad Aut\u00f3noma de Madrid (UAM) and Instituto de Investigaciones Biom\u00e9dicas \u2019Alberto Sols\u2019 (CSIC-UAM) , Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Departamento de Bioqu\u00edmica, Universidad Aut\u00f3noma de Madrid (UAM) and Instituto de Investigaciones Biom\u00e9dicas \u2019Alberto Sols\u2019 (CSIC-UAM) , Madrid, Spain","institution_ids":["https://openalex.org/I4210091816","https://openalex.org/I63634437"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026664289","display_name":"Wyeth W. Wasserman","orcid":"https://orcid.org/0000-0001-6098-6412"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I4210162161","display_name":"Child and Family Research Institute","ror":"https://ror.org/04yqm9y25","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210162161"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Wyeth W Wasserman","raw_affiliation_strings":["Department of Medical Genetics, University of British Columbia Vancouver, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute , Vancouver, BC V5Z 4H4, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Medical Genetics, University of British Columbia Vancouver, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute , Vancouver, BC V5Z 4H4, Canada","institution_ids":["https://openalex.org/I4210162161","https://openalex.org/I141945490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003566291","display_name":"Luis del Peso","orcid":"https://orcid.org/0000-0003-4014-5688"},"institutions":[{"id":"https://openalex.org/I2800562746","display_name":"Hospital Universitario La Paz","ror":"https://ror.org/01s1q0w69","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I2800562746"]},{"id":"https://openalex.org/I2801357902","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886","country_code":"ES","type":"funder","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210091816","display_name":"Instituto de Investigaciones Biom\u00e9dicas Sols-Morreale","ror":"https://ror.org/00ha1f767","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I4210091816","https://openalex.org/I63634437"]},{"id":"https://openalex.org/I4210099160","display_name":"Centro de Investigaci\u00f3n Biom\u00e9dica en Red de Enfermedades Respiratorias","ror":"https://ror.org/0119pby33","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801357902","https://openalex.org/I4210099160","https://openalex.org/I4210115082","https://openalex.org/I4387152914"]},{"id":"https://openalex.org/I4210103477","display_name":"Hospital La Paz Institute for Health Research","ror":"https://ror.org/017bynh47","country_code":"ES","type":"facility","lineage":["https://openalex.org/I4210103477"]},{"id":"https://openalex.org/I63634437","display_name":"Universidad Aut\u00f3noma de Madrid","ror":"https://ror.org/01cby8j38","country_code":"ES","type":"education","lineage":["https://openalex.org/I63634437"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Luis del Peso","raw_affiliation_strings":["CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III , Madrid, Spain","Departamento de Bioqu\u00edmica, Universidad Aut\u00f3noma de Madrid (UAM) and Instituto de Investigaciones Biom\u00e9dicas \u2019Alberto Sols\u2019 (CSIC-UAM) , Madrid, Spain","IdiPaz, Instituto de Investigaci\u00f3n Sanitaria del Hospital Universitario La Paz"],"affiliations":[{"raw_affiliation_string":"CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III , Madrid, Spain","institution_ids":["https://openalex.org/I4210099160","https://openalex.org/I2801357902"]},{"raw_affiliation_string":"Departamento de Bioqu\u00edmica, Universidad Aut\u00f3noma de Madrid (UAM) and Instituto de Investigaciones Biom\u00e9dicas \u2019Alberto Sols\u2019 (CSIC-UAM) , Madrid, Spain","institution_ids":["https://openalex.org/I4210091816","https://openalex.org/I63634437"]},{"raw_affiliation_string":"IdiPaz, Instituto de Investigaci\u00f3n Sanitaria del Hospital Universitario La Paz","institution_ids":["https://openalex.org/I4210103477","https://openalex.org/I2800562746"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003566291"],"corresponding_institution_ids":["https://openalex.org/I2800562746","https://openalex.org/I2801357902","https://openalex.org/I4210091816","https://openalex.org/I4210099160","https://openalex.org/I4210103477","https://openalex.org/I63634437"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.8341,"has_fulltext":true,"cited_by_count":54,"citation_normalized_percentile":{"value":0.91642825,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"35","issue":"24","first_page":"5339","last_page":"5340"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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/T10604","display_name":"RNA Research and Splicing","score":0.998199999332428,"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/chip","display_name":"Chip","score":0.6551169157028198},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6203961372375488},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5700992345809937},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4939451813697815},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4479314386844635},{"id":"https://openalex.org/keywords/factor","display_name":"Factor (programming language)","score":0.4166058897972107},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3261779546737671},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.32113415002822876},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23590216040611267},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20386859774589539},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20221462845802307},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1388912796974182},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13614404201507568},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.07165396213531494}],"concepts":[{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.6551169157028198},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6203961372375488},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5700992345809937},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4939451813697815},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4479314386844635},{"id":"https://openalex.org/C2781039887","wikidata":"https://www.wikidata.org/wiki/Q1391724","display_name":"Factor (programming language)","level":2,"score":0.4166058897972107},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3261779546737671},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.32113415002822876},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23590216040611267},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20386859774589539},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20221462845802307},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1388912796974182},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13614404201507568},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.07165396213531494}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","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":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5339/48978133/bioinformatics_35_24_5339.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"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:31347689","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31347689","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},{"id":"pmh:oai:repositorio.uam.es:10486/691891","is_oa":true,"landing_page_url":"http://hdl.handle.net/10486/691891","pdf_url":null,"source":{"id":"https://openalex.org/S4306400963","display_name":"Biblos-e Archivo (Universidad Aut\u00f3noma de Madrid)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63634437","host_organization_name":"Universidad Aut\u00f3noma de Madrid","host_organization_lineage":["https://openalex.org/I63634437"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btz573","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz573","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/24/5339/48978133/bioinformatics_35_24_5339.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"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":[{"id":"https://openalex.org/G353571274","display_name":null,"funder_award_id":"SAF2014-53819-R","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"},{"id":"https://openalex.org/G5650843047","display_name":null,"funder_award_id":"SAF2017-88771-R","funder_id":"https://openalex.org/F4320322930","funder_display_name":"Ministerio de Ciencia e Innovaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320313831","display_name":"Comunidad de Madrid","ror":null},{"id":"https://openalex.org/F4320321889","display_name":"Fundaci\u00f3n Caja Madrid","ror":null},{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2964526879.pdf","grobid_xml":"https://content.openalex.org/works/W2964526879.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1979594866","https://openalex.org/W2010457001","https://openalex.org/W2070050178","https://openalex.org/W2098023402","https://openalex.org/W2107281049","https://openalex.org/W2108390464","https://openalex.org/W2130410032","https://openalex.org/W2158485480","https://openalex.org/W2572986783","https://openalex.org/W2606675097","https://openalex.org/W2767743008","https://openalex.org/W2772692099","https://openalex.org/W2952990620","https://openalex.org/W6653110446"],"related_works":["https://openalex.org/W2003033456","https://openalex.org/W2317123011","https://openalex.org/W2386246912","https://openalex.org/W4250911175","https://openalex.org/W2036193034","https://openalex.org/W2037330166","https://openalex.org/W1995066794","https://openalex.org/W2355270116","https://openalex.org/W2090256089","https://openalex.org/W2374439519"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
