{"id":"https://openalex.org/W2118238076","doi":"https://doi.org/10.1186/1471-2105-11-s11-s5","title":"TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information","display_name":"TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information","publication_year":2010,"publication_date":"2010-12-01","ids":{"openalex":"https://openalex.org/W2118238076","doi":"https://doi.org/10.1186/1471-2105-11-s11-s5","mag":"2118238076","pmid":"https://pubmed.ncbi.nlm.nih.gov/21172055"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-s11-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s11-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S11-S5","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/10.1186/1471-2105-11-S11-S5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014353485","display_name":"Qi Liu","orcid":"https://orcid.org/0000-0002-0596-5579"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qi Liu","raw_affiliation_strings":["School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. liuqi@sjtu.edu.cn","School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China. liuqi@sjtu.edu.cn","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001780861","display_name":"Yejun Tan","orcid":"https://orcid.org/0009-0000-9567-0186"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yejun Tan","raw_affiliation_strings":["Merck Research Laboratory, Rahway, NJ, 07065, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratory, Rahway, NJ, 07065, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025077602","display_name":"Tao Huang","orcid":"https://orcid.org/0000-0003-1975-9693"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Huang","raw_affiliation_strings":["Shanghai Center for Bioinformation Technology, Shanghai, 200235, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Center for Bioinformation Technology, Shanghai, 200235, China","institution_ids":["https://openalex.org/I4210162648"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076249394","display_name":"Guohui Ding","orcid":"https://orcid.org/0000-0002-2888-1335"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guohui Ding","raw_affiliation_strings":["Shanghai Center for Bioinformation Technology, Shanghai, 200235, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Center for Bioinformation Technology, Shanghai, 200235, China","institution_ids":["https://openalex.org/I4210162648"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000803372","display_name":"Zhidong Tu","orcid":"https://orcid.org/0000-0001-7721-1410"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhidong Tu","raw_affiliation_strings":["Merck Research Laboratory, Boston, MA, 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratory, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115602441","display_name":"Lei Liu","orcid":"https://orcid.org/0000-0002-4604-4629"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Liu","raw_affiliation_strings":["Shanghai Center for Bioinformation Technology, Shanghai, 200235, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Center for Bioinformation Technology, Shanghai, 200235, China","institution_ids":["https://openalex.org/I4210162648"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008280608","display_name":"Yixue Li","orcid":"https://orcid.org/0000-0002-1198-7176"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yixue Li","raw_affiliation_strings":["School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","Shanghai Center for Bioinformation Technology, Shanghai, 200235, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Shanghai Center for Bioinformation Technology, Shanghai, 200235, China","institution_ids":["https://openalex.org/I4210162648"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101790056","display_name":"Hongyue Dai","orcid":"https://orcid.org/0000-0002-6609-9141"},"institutions":[{"id":"https://openalex.org/I1285764155","display_name":"Merck & Co., Inc., Rahway, NJ, USA (United States)","ror":"https://ror.org/02891sr49","country_code":"US","type":"company","lineage":["https://openalex.org/I1285764155"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hongyue Dai","raw_affiliation_strings":["Merck Research Laboratory, Boston, MA, 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck Research Laboratory, Boston, MA, 02115, USA","institution_ids":["https://openalex.org/I1285764155"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033203853","display_name":"Lu Xie","orcid":"https://orcid.org/0000-0001-7541-2243"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lu Xie","raw_affiliation_strings":["Shanghai Center for Bioinformation Technology, Shanghai, 200235, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Center for Bioinformation Technology, Shanghai, 200235, China","institution_ids":["https://openalex.org/I4210162648"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014353485","https://openalex.org/A5033203853","https://openalex.org/A5101790056"],"corresponding_institution_ids":["https://openalex.org/I1285764155","https://openalex.org/I183067930","https://openalex.org/I4210162648"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6712,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.69473804,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"11","issue":"S11","first_page":"S5","last_page":"S5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.35690000653266907,"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":0.35690000653266907,"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":0.10440000146627426,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.08749999850988388,"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/downstream","display_name":"Downstream (manufacturing)","score":0.6654636263847351},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6600339412689209},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5178387761116028},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49166232347488403},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4785371720790863},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4513513147830963},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.4456968307495117},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4331483840942383},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.41039901971817017},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3611508905887604},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.32676762342453003},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3068636953830719},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11008378863334656},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08327797055244446}],"concepts":[{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.6654636263847351},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6600339412689209},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5178387761116028},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49166232347488403},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4785371720790863},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4513513147830963},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.4456968307495117},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4331483840942383},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.41039901971817017},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3611508905887604},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32676762342453003},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3068636953830719},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11008378863334656},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08327797055244446},{"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/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005285","descriptor_name":"Fermentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005990","descriptor_name":"Glycerol","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005990","descriptor_name":"Glycerol","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005990","descriptor_name":"Glycerol","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017353","descriptor_name":"Gene Deletion","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-11-s11-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s11-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S11-S5","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:21172055","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21172055","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:doaj.org/article:cd155eb1e5c74fad80051be441c26d14","is_oa":false,"landing_page_url":"https://doaj.org/article/cd155eb1e5c74fad80051be441c26d14","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 11, Iss Suppl 11, p S5 (2010)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3024863","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3024863","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-s11-s5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-s11-s5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-S11-S5","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":[{"id":"https://openalex.org/G1842644662","display_name":null,"funder_award_id":"60874105","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4393023279","display_name":null,"funder_award_id":"2009CB918404","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4506771890","display_name":"\u57fa\u4e8e\u591a\u79cd\u751f\u7269\u5b66\u6570\u636e\u6574\u5408\u7684\u57fa\u56e0\u8c03\u63a7\u7f51\u7edc\u91cd\u6784\u7814\u7a76","funder_award_id":"30700154","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5571052226","display_name":null,"funder_award_id":"2006CB910700","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8508431015","display_name":null,"funder_award_id":"31070752","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320309151","display_name":"Vanderbilt University","ror":"https://ror.org/02vm5rt34"},{"id":"https://openalex.org/F4320309601","display_name":"Vanderbilt-Ingram Cancer Center","ror":"https://ror.org/05dq2gs74"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2118238076.pdf","grobid_xml":"https://content.openalex.org/works/W2118238076.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W1753000577","https://openalex.org/W1967490380","https://openalex.org/W1972129511","https://openalex.org/W1974220691","https://openalex.org/W1975397478","https://openalex.org/W1977186059","https://openalex.org/W1984000968","https://openalex.org/W1990235046","https://openalex.org/W1994605750","https://openalex.org/W1999084705","https://openalex.org/W2020239072","https://openalex.org/W2036515140","https://openalex.org/W2045519885","https://openalex.org/W2046081872","https://openalex.org/W2053126761","https://openalex.org/W2058413336","https://openalex.org/W2077667351","https://openalex.org/W2077941487","https://openalex.org/W2077953882","https://openalex.org/W2079499741","https://openalex.org/W2080564499","https://openalex.org/W2083869247","https://openalex.org/W2084544581","https://openalex.org/W2084619201","https://openalex.org/W2097090208","https://openalex.org/W2099189600","https://openalex.org/W2100445710","https://openalex.org/W2102247469","https://openalex.org/W2103274097","https://openalex.org/W2106414909","https://openalex.org/W2107297328","https://openalex.org/W2111182449","https://openalex.org/W2113976732","https://openalex.org/W2117409112","https://openalex.org/W2118260141","https://openalex.org/W2120930467","https://openalex.org/W2123600940","https://openalex.org/W2128987420","https://openalex.org/W2130508212","https://openalex.org/W2133045519","https://openalex.org/W2137683543","https://openalex.org/W2137896695","https://openalex.org/W2139025111","https://openalex.org/W2140541235","https://openalex.org/W2140593394","https://openalex.org/W2142409266","https://openalex.org/W2143944135","https://openalex.org/W2146206618","https://openalex.org/W2150182123","https://openalex.org/W2154022964","https://openalex.org/W2154475586","https://openalex.org/W2157717340","https://openalex.org/W2157764088","https://openalex.org/W2158107150","https://openalex.org/W2165054897","https://openalex.org/W2166606182","https://openalex.org/W2168797545","https://openalex.org/W2169983745","https://openalex.org/W2170778160","https://openalex.org/W4239029175"],"related_works":["https://openalex.org/W106077234","https://openalex.org/W2041374557","https://openalex.org/W2081929287","https://openalex.org/W2132561013","https://openalex.org/W2144348650","https://openalex.org/W1994852842","https://openalex.org/W4246178523","https://openalex.org/W2613929436","https://openalex.org/W2347793859","https://openalex.org/W3151254369"],"abstract_inverted_index":{"BACKGROUND:":[0],"Inference":[1],"of":[2,14,29,46,53,60,96,122,171,185,227,240,268,315],"causal":[3,77,310],"regulators":[4,78,311],"responsible":[5,79,264],"for":[6,80,106,265,272,294,303],"gene":[7,69,94,305],"expression":[8,37,81,120,306],"changes":[9,239],"under":[10],"different":[11],"conditions":[12],"is":[13],"great":[15],"importance":[16],"but":[17,104],"remains":[18],"rather":[19],"challenging.":[20],"To":[21],"date,":[22],"most":[23],"approaches":[24],"use":[25],"direct":[26,255],"binding":[27,44],"targets":[28,45],"transcription":[30,258],"factors":[31],"(TFs)":[32],"to":[33,74,90,181,215,254,291,308],"associate":[34],"TFs":[35,153,163,202,208,243,269,273,276],"with":[36,137],"profiles.":[38],"However,":[39],"the":[40,50,54,58,107,138,183,211,221,235,266,313],"low":[41],"overlap":[42],"between":[43],"a":[47,66,97,300],"TF":[48,55,98,124,131,134,156,286],"and":[49,86,126,133,159,177,192,203,219,229,259,318],"affected":[51],"genes":[52],"knockout":[56,125,132,157],"limits":[57],"power":[59,184],"those":[61],"methods.":[62],"RESULTS:":[63],"We":[64,83,114],"developed":[65],"TF-centered":[67],"downstream":[68,93,170],"set":[70],"enrichment":[71],"analysis":[72],"approach":[73],"identify":[75,309],"potential":[76,207],"changes.":[82],"constructed":[84],"hierarchical":[85],"multi-layer":[87],"regulation":[88,187,225,261,287],"models":[89,188,288],"derive":[91],"possible":[92],"sets":[95],"using":[99,141],"not":[100],"only":[101],"TF-DNA":[102,142,190,316],"interactions,":[103],"also,":[105],"first":[108],"time,":[109],"post-translational":[110,260],"modifications":[111],"(PTM)":[112],"information.":[113,194,320],"verified":[115],"our":[116,145,196,279],"method":[117,146,197,280,298],"in":[118,154,164,210,220,252,312],"one":[119],"dataset":[121,128],"large-scale":[123,155],"another":[127],"involving":[129],"both":[130],"overexpression.":[135,274],"Compared":[136],"flat":[139],"model":[140],"interactions":[143,191,317],"alone,":[144],"correctly":[147],"identified":[148,199],"five":[149],"more":[150,161],"actual":[151],"perturbed":[152,162,173],"data":[158,307],"six":[160],"overexpression":[165],"data.":[166],"Potential":[167],"regulatory":[168],"pathways":[169,226],"three":[172],"regulators-":[174],"SNF1,":[175],"AFT1":[176,230],"SUT1":[178,228],"-were":[179],"given":[180],"demonstrate":[182],"multilayer":[186],"integrating":[189],"PTM":[193,319],"Additionally,":[195],"successfully":[198],"known":[200],"important":[201],"inferred":[204,277],"some":[205],"novel":[206],"involved":[209],"transition":[212],"from":[213],"fermentative":[214],"glycerol-based":[216],"respiratory":[217],"growth":[218],"pheromone":[222],"response.":[223],"Downstream":[224],"were":[231],"also":[232,263],"supported":[233,282],"by":[234,278,283],"mRNA":[236],"and/or":[237,244],"phosphorylation":[238],"their":[241],"mediating":[242],"\"modulator\"":[245],"proteins.":[246],"CONCLUSIONS:":[247],"The":[248],"results":[249],"suggest":[250],"that":[251],"addition":[253],"transcription,":[256],"indirect":[257],"are":[262,281],"effects":[267],"perturbation,":[270],"especially":[271],"Many":[275],"literature.":[284],"Multiple":[285],"could":[289],"lead":[290],"new":[292],"hypotheses":[293],"future":[295],"experiments.":[296],"Our":[297],"provides":[299],"valuable":[301],"framework":[302],"analyzing":[304],"context":[314]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}