{"id":"https://openalex.org/W3160569367","doi":"https://doi.org/10.1093/bioinformatics/btab379","title":"MotifGenie: a Python application for searching transcription factor binding sequences using ChIP-Seq datasets","display_name":"MotifGenie: a Python application for searching transcription factor binding sequences using ChIP-Seq datasets","publication_year":2021,"publication_date":"2021-05-13","ids":{"openalex":"https://openalex.org/W3160569367","doi":"https://doi.org/10.1093/bioinformatics/btab379","mag":"3160569367","pmid":"https://pubmed.ncbi.nlm.nih.gov/33999190"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab379","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab379","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032616122","display_name":"\u00c7era\u011f O\u011fuzt\u00fcz\u00fcn","orcid":"https://orcid.org/0009-0008-3134-3379"},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Cerag Oguztuzun","raw_affiliation_strings":["Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Bilkent University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088580990","display_name":"Pelin Ya\u015far","orcid":"https://orcid.org/0000-0003-3027-9842"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Pelin Yasar","raw_affiliation_strings":["Department of Biological Sciences, Middle East Technical University , Ankara 06800, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Middle East Technical University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I201799495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083046898","display_name":"Kerim Yavuz","orcid":"https://orcid.org/0000-0003-4980-8804"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Kerim Yavuz","raw_affiliation_strings":["Department of Biological Sciences, Middle East Technical University , Ankara 06800, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Middle East Technical University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I201799495"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032473959","display_name":"Mesut Muyan","orcid":"https://orcid.org/0000-0003-3058-6228"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Mesut Muyan","raw_affiliation_strings":["Department of Biological Sciences, Middle East Technical University , Ankara 06800, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Middle East Technical University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I201799495"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045764563","display_name":"Tolga Can","orcid":"https://orcid.org/0000-0002-5532-0154"},"institutions":[{"id":"https://openalex.org/I201799495","display_name":"Middle East Technical University","ror":"https://ror.org/014weej12","country_code":"TR","type":"education","lineage":["https://openalex.org/I201799495"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Tolga Can","raw_affiliation_strings":["Department of Computer Engineering, Middle East Technical University , Ankara 06800, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-5532-0154","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Middle East Technical University , Ankara 06800, Turkey","institution_ids":["https://openalex.org/I201799495"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045764563"],"corresponding_institution_ids":["https://openalex.org/I201799495"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3172,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.54430616,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"37","issue":"22","first_page":"4238","last_page":"4239"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9448000192642212,"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":0.9448000192642212,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0071000000461936,"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":0.006500000134110451,"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/python","display_name":"Python (programming language)","score":0.921331524848938},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6754776239395142},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4940636456012726},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47112131118774414},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4634760320186615},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3441448509693146},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2627633213996887},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1979764699935913},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13065105676651},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12611433863639832}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.921331524848938},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6754776239395142},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4940636456012726},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47112131118774414},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4634760320186615},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3441448509693146},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2627633213996887},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1979764699935913},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13065105676651},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12611433863639832}],"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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab379","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab379","pdf_url":null,"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:33999190","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33999190","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:https://open.metu.edu.tr:11511/92660","is_oa":false,"landing_page_url":"https://hdl.handle.net/11511/92660","pdf_url":null,"source":{"id":"https://openalex.org/S4306402495","display_name":"OpenMETU (Middle East Technical University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I201799495","host_organization_name":"Middle East Technical University","host_organization_lineage":["https://openalex.org/I201799495"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/77240","is_oa":false,"landing_page_url":"http://hdl.handle.net/11693/77240","pdf_url":null,"source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.5199999809265137,"id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W2066167693","https://openalex.org/W2125362831","https://openalex.org/W2128016314","https://openalex.org/W2171808845","https://openalex.org/W2346143774","https://openalex.org/W2796842840","https://openalex.org/W2988716798","https://openalex.org/W3191795524","https://openalex.org/W6769944288","https://openalex.org/W6799867698"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W3193760048","https://openalex.org/W4285822516","https://openalex.org/W2551200859"],"abstract_inverted_index":{"MOTIVATION:":[0],"Next":[1],"generation":[2],"sequencing":[3],"enabled":[4],"the":[5,23,37,50,99,123,126,165],"fast":[6],"accumulation":[7],"of":[8,25,39,49,64,77,86,113,146,160],"genomic":[9,144],"data":[10,60],"at":[11,191],"public":[12],"repositories.":[13],"This":[14],"technology":[15],"also":[16],"made":[17],"it":[18],"possible":[19],"to":[20,56,117],"better":[21],"understand":[22],"regulation":[24],"gene":[26],"expression":[27],"by":[28,92,131,181],"transcription":[29],"factors":[30],"(TFs)":[31],"and":[32,58,88,98,137,176],"various":[33],"chromatin-associated":[34],"proteins":[35],"through":[36],"integration":[38],"chromatin":[40],"immunoprecipitation":[41],"(ChIP-Seq).":[42],"The":[43],"Cistrome":[44,93,127],"Project":[45],"has":[46],"become":[47],"one":[48],"indispensable":[51],"research":[52],"portals":[53],"for":[54,109,134,153],"biologists":[55,175],"access":[57],"analyze":[59],"generated":[61],"with":[62,173],"thousands":[63],"ChIP-Seq":[65,119],"experiments.":[66,120,183],"Integrative":[67],"motif":[68,159],"analysis":[69,89],"on":[70],"shared":[71,139],"binding":[72,111,154,158],"regions":[73,141,152],"among":[74],"a":[75,84,105,114,143,157,161],"set":[76,85],"experiments":[78],"is":[79,169,188],"not":[80],"yet":[81],"achievable":[82],"despite":[83],"search":[87],"tools":[90],"provided":[91],"via":[94],"its":[95,177],"web":[96],"interface":[97],"Galaxy":[100],"framework.":[101],"RESULTS:":[102],"We":[103,121,148],"implemented":[104],"python":[106],"command-line":[107],"tool":[108],"searching":[110],"sequences":[112,155],"TF":[115,162],"common":[116],"multiple":[118],"use":[122],"peaks":[124],"in":[125,142,171],"database":[128],"as":[129],"identified":[130],"MACS":[132],"2.0":[133],"each":[135],"experiment":[136],"identify":[138],"peak":[140],"locus":[145],"interest.":[147],"then":[149],"scan":[150],"these":[151],"using":[156],"obtained":[163],"from":[164],"JASPAR":[166],"database.":[167],"MotifGenie":[168,187],"developed":[170],"collaboration":[172],"molecular":[174],"findings":[178],"are":[179],"corroborated":[180],"laboratory":[182],"AVAILABILITY":[184],"AND":[185],"IMPLEMENTATION:":[186],"freely":[189],"available":[190],"https://github.com/ceragoguztuzun/MotifGenie.":[192]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
