{"id":"https://openalex.org/W2116744176","doi":"https://doi.org/10.1186/1752-0509-6-102","title":"Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data","display_name":"Identifying biologically interpretable transcription factor knockout targets by jointly analyzing the transcription factor knockout microarray and the ChIP-chip data","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W2116744176","doi":"https://doi.org/10.1186/1752-0509-6-102","mag":"2116744176","pmid":"https://pubmed.ncbi.nlm.nih.gov/22898448"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-102","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-102","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-102","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-102","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028273823","display_name":"Tzu-Hsien Yang","orcid":"https://orcid.org/0000-0001-9420-196X"},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Tzu-Hsien Yang","raw_affiliation_strings":["Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan","Department of Electrical Engineering, National Cheng Kung University, Tainan (Taiwan)"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan","institution_ids":["https://openalex.org/I91807558"]},{"raw_affiliation_string":"Department of Electrical Engineering, National Cheng Kung University, Tainan (Taiwan)","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110213729","display_name":"Wei Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Wei-Sheng Wu","raw_affiliation_strings":["Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan","Department of Electrical Engineering, National Cheng Kung University, Tainan (Taiwan)"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan","institution_ids":["https://openalex.org/I91807558"]},{"raw_affiliation_string":"Department of Electrical Engineering, National Cheng Kung University, Tainan (Taiwan)","institution_ids":["https://openalex.org/I91807558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5028273823"],"corresponding_institution_ids":["https://openalex.org/I91807558"],"apc_list":null,"apc_paid":null,"fwci":1.3446,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.80065949,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"6","issue":"1","first_page":"102","last_page":"102"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9995999932289124,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9995999932289124,"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":0.9984999895095825,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9950000047683716,"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/transcription-factor","display_name":"Transcription factor","score":0.7201382517814636},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6115869879722595},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5410906076431274},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.5359163284301758},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5077618360519409},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.48813971877098083},{"id":"https://openalex.org/keywords/chip","display_name":"Chip","score":0.4742487967014313},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4615499973297119},{"id":"https://openalex.org/keywords/factor","display_name":"Factor (programming language)","score":0.4237593412399292},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.4229240119457245},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.36743608117103577},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2670961320400238},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19402951002120972},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1702013611793518},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.08304443955421448}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.7201382517814636},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6115869879722595},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5410906076431274},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.5359163284301758},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5077618360519409},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.48813971877098083},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.4742487967014313},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4615499973297119},{"id":"https://openalex.org/C2781039887","wikidata":"https://www.wikidata.org/wiki/Q1391724","display_name":"Factor (programming language)","level":2,"score":0.4237593412399292},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.4229240119457245},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.36743608117103577},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2670961320400238},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19402951002120972},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1702013611793518},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.08304443955421448},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000172","qualifier_name":"deficiency","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000172","qualifier_name":"deficiency","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000172","qualifier_name":"deficiency","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":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","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":true},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","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":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055786","descriptor_name":"Gene Knockout Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055786","descriptor_name":"Gene Knockout Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055786","descriptor_name":"Gene Knockout Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-6-102","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-102","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-102","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},{"id":"pmid:22898448","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22898448","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 systems biology","raw_type":null},{"id":"pmh:oai:europepmc.org:2463421","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3465233","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-102","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-102","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-102","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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 Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8737284672","display_name":null,"funder_award_id":"NSC 99","funder_id":"https://openalex.org/F4320321040","funder_display_name":"National Science Council"}],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2116744176.pdf","grobid_xml":"https://content.openalex.org/works/W2116744176.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1483463110","https://openalex.org/W1588911128","https://openalex.org/W1806630989","https://openalex.org/W1990072661","https://openalex.org/W1997183178","https://openalex.org/W2019012779","https://openalex.org/W2077941487","https://openalex.org/W2077953882","https://openalex.org/W2079499741","https://openalex.org/W2080498142","https://openalex.org/W2080564499","https://openalex.org/W2081098333","https://openalex.org/W2098054200","https://openalex.org/W2099788003","https://openalex.org/W2102055689","https://openalex.org/W2102221598","https://openalex.org/W2107233900","https://openalex.org/W2107598685","https://openalex.org/W2110328538","https://openalex.org/W2116578996","https://openalex.org/W2116811581","https://openalex.org/W2126602684","https://openalex.org/W2140082959","https://openalex.org/W2143944135","https://openalex.org/W2154475586","https://openalex.org/W2158128075","https://openalex.org/W2163797429","https://openalex.org/W2166574880","https://openalex.org/W2166953436","https://openalex.org/W2167190345","https://openalex.org/W2169251996","https://openalex.org/W2331642764","https://openalex.org/W2351024354","https://openalex.org/W2915108429","https://openalex.org/W3145128584","https://openalex.org/W4252684946"],"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":{"By":[0],"jointly":[1],"analyzing":[2],"the":[3,12,22,27,41,66],"TFKM":[4],"and":[5],"ChIP-chip":[6],"data,":[7],"our":[8,59],"method":[9],"can":[10],"extract":[11],"biologically":[13],"interpretable":[14],"TF":[15,23,29,47],"knockout":[16,51],"targets":[17],"by":[18,58],"identifying":[19],"paths":[20,35],"(in":[21],"binding":[24],"network)":[25],"from":[26],"knocked-out":[28],"to":[30,80],"these":[31],"targets.":[32,52],"The":[33],"identified":[34],"form":[36],"experimentally":[37,63],"testable":[38],"hypotheses":[39,56],"regarding":[40],"molecular":[42],"mechanisms":[43],"of":[44],"how":[45],"a":[46,77],"may":[48],"regulate":[49],"its":[50],"About":[53],"seven":[54],"hundred":[55],"generated":[57],"methods":[60],"have":[61],"been":[62],"validated":[64],"in":[65],"literature.":[67],"Our":[68],"work":[69],"demonstrates":[70],"that":[71],"integrating":[72],"different":[73],"data":[74],"sources":[75],"is":[76],"powerful":[78],"approach":[79],"study":[81],"complex":[82],"biological":[83],"systems.":[84]},"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":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}