{"id":"https://openalex.org/W2108901799","doi":"https://doi.org/10.1186/1471-2105-11-511","title":"Trimming of mammalian transcriptional networks using network component analysis","display_name":"Trimming of mammalian transcriptional networks using network component analysis","publication_year":2010,"publication_date":"2010-10-13","ids":{"openalex":"https://openalex.org/W2108901799","doi":"https://doi.org/10.1186/1471-2105-11-511","mag":"2108901799","pmid":"https://pubmed.ncbi.nlm.nih.gov/20942926"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-11-511","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-511","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-511","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/10.1186/1471-2105-11-511","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053537520","display_name":"Linh M. Tran","orcid":"https://orcid.org/0000-0001-8597-643X"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Linh M Tran","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095-1592, USA","Department of Chemical and Biomolecular Engineering University of California Los Angeles USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095-1592, USA","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering University of California Los Angeles USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044507284","display_name":"Daniel R. Hyduke","orcid":null},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel R Hyduke","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095-1592, USA","Department of Chemical and Biomolecular Engineering University of California Los Angeles USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095-1592, USA","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering University of California Los Angeles USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007847950","display_name":"James C. Liao","orcid":"https://orcid.org/0000-0002-4580-7276"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"James C Liao","raw_affiliation_strings":["Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095-1592, USA","Department of Chemical and Biomolecular Engineering University of California Los Angeles USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095-1592, USA","institution_ids":["https://openalex.org/I161318765"]},{"raw_affiliation_string":"Department of Chemical and Biomolecular Engineering University of California Los Angeles USA","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5007847950"],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.9964,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.7431844,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"11","issue":"1","first_page":"511","last_page":"511"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6402999758720398,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6402999758720398,"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":0.24719999730587006,"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":0.04479999840259552,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.7399675846099854},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6583162546157837},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6512006521224976},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6049154996871948},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5640576481819153},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.5230346918106079},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5190870761871338},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.5124614834785461},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5006489753723145},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.49145519733428955},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.4171147346496582},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4068753123283386},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.30259472131729126}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7399675846099854},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6583162546157837},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6512006521224976},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6049154996871948},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5640576481819153},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.5230346918106079},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5190870761871338},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.5124614834785461},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5006489753723145},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.49145519733428955},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.4171147346496582},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4068753123283386},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.30259472131729126}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-11-511","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-511","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-511","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:20942926","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20942926","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:pubmedcentral.nih.gov:2967563","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2967563","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"},{"id":"pmh:oai:doaj.org/article:0f2d8e5f96584e03b4089d068b82cca0","is_oa":false,"landing_page_url":"https://doaj.org/article/0f2d8e5f96584e03b4089d068b82cca0","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 1, p 511 (2010)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt0dj9882s","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/0dj9882s","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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 1","raw_type":"article"},{"id":"pmh:qt0dj9882s","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/0dj9882s","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Tran, Linh M; Hyduke, Daniel R; &amp; Liao, James C. (2010). Trimming of mammalian transcriptional networks using network component analysis. BMC Bioinformatics, 11(1), 511. doi: http://dx.doi.org/10.1186/1471-2105-11-511. Retrieved from: http://www.escholarship.org/uc/item/0dj9882s","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-11-511","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-11-511","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-11-511","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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G4656389570","display_name":null,"funder_award_id":"GM076143","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2108901799.pdf","grobid_xml":"https://content.openalex.org/works/W2108901799.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W114905856","https://openalex.org/W1499561015","https://openalex.org/W1576403695","https://openalex.org/W1640418706","https://openalex.org/W1753000577","https://openalex.org/W1966630774","https://openalex.org/W1968371014","https://openalex.org/W1971470015","https://openalex.org/W1975160071","https://openalex.org/W2009899164","https://openalex.org/W2025166348","https://openalex.org/W2062997257","https://openalex.org/W2069645361","https://openalex.org/W2080395830","https://openalex.org/W2080498142","https://openalex.org/W2085595936","https://openalex.org/W2105282404","https://openalex.org/W2107209294","https://openalex.org/W2120893886","https://openalex.org/W2122305079","https://openalex.org/W2122683221","https://openalex.org/W2125512776","https://openalex.org/W2128424082","https://openalex.org/W2135805255","https://openalex.org/W2142433578","https://openalex.org/W2143427623","https://openalex.org/W2144710927","https://openalex.org/W2148541040","https://openalex.org/W2152824658","https://openalex.org/W2153073444","https://openalex.org/W2154807836","https://openalex.org/W2155120241","https://openalex.org/W2157983986","https://openalex.org/W2162491638","https://openalex.org/W2164895949","https://openalex.org/W2167123367","https://openalex.org/W2170567460","https://openalex.org/W2171322586"],"related_works":["https://openalex.org/W1985116998","https://openalex.org/W2588404065","https://openalex.org/W2371696992","https://openalex.org/W2106018309","https://openalex.org/W2035892324","https://openalex.org/W4327811409","https://openalex.org/W2111172999","https://openalex.org/W2563598809","https://openalex.org/W1964561434","https://openalex.org/W2108901799"],"abstract_inverted_index":{"BACKGROUND:":[0],"Network":[1],"Component":[2],"Analysis":[3],"(NCA)":[4],"has":[5,331],"been":[6,332],"used":[7],"to":[8,54,90,238,267,296,334,338,357],"deduce":[9],"the":[10,21,26,60,96,101,104,109,118,126,140,148,178,189,201,214,232,262,285,297,306,311,319,353,358],"activities":[11],"of":[12,80,139,151,158,200,218,246,259,274,291,321,355,360],"transcription":[13],"factors":[14],"(TFs)":[15],"from":[16,168,177],"gene":[17,78],"expression":[18],"data":[19,166],"and":[20,34,42,77,103,108,155,185,191,205,254],"TF-gene":[22,27,57,308,313],"binding":[23],"relationship.":[24],"However,":[25],"interaction":[28,278],"varies":[29],"in":[30,72,82,125,147,223,231],"different":[31],"environmental":[32],"conditions":[33],"tissues,":[35],"but":[36],"such":[37,94,325],"information":[38,68],"is":[39,52,300,315],"rarely":[40],"available":[41],"cannot":[43],"be":[44,70,281],"predicted":[45,146],"simply":[46],"by":[47],"motif":[48],"analysis.":[49,364],"Thus,":[50,349],"it":[51],"beneficial":[53],"identify":[55,305],"key":[56,74,277],"interactions":[58,99,314],"under":[59,170,213],"experimental":[61,215],"condition":[62,150],"based":[63],"on":[64],"transcriptome":[65,132,165],"data.":[66],"Such":[67],"would":[69],"useful":[71],"identifying":[73],"regulatory":[75,98,110,119,286,362],"pathways":[76,229],"markers":[79],"TFs":[81,102,190,208,220,344],"further":[83],"studies.":[84],"RESULTS:":[85],"We":[86],"developed":[87,333],"an":[88,271],"algorithm":[89,161,303,330,351],"trim":[91],"network":[92,175,264,363],"connectivity":[93],"that":[95,117,301],"important":[97,272,307,312],"between":[100,188],"genes":[105,143],"were":[106,112,121,134,144],"retained":[107,195],"signals":[111,120],"deduced.":[113],"Theoretical":[114],"studies":[115],"demonstrated":[116],"accurately":[122],"reconstructed":[123],"even":[124],"case":[127],"where":[128,342],"only":[129],"three":[130],"independent":[131],"datasets":[133],"available.":[135],"At":[136],"least":[137],"80%":[138],"main":[141],"target":[142,273],"correctly":[145],"extreme":[149],"high":[152],"noise":[153],"level":[154],"small":[156],"number":[157],"datasets.":[159],"Our":[160,193],"was":[162,265],"tested":[163],"with":[164,241],"taken":[167],"mice":[169],"rapamycin":[171],"treatment.":[172],"The":[173,289],"initial":[174],"topology":[176],"literature":[179],"contains":[180],"70":[181],"TFs,":[182,248],"778":[183],"genes,":[184],"1423":[186],"edges":[187,197],"genes.":[192],"method":[194],"1074":[196],"(i.e.":[198],"75%":[199],"original":[202,298],"edge":[203],"number)":[204],"identified":[206],"17":[207],"as":[209,270,326],"being":[210],"significantly":[211],"perturbed":[212],"condition.":[216],"Twelve":[217],"these":[219,247],"are":[221,236,250,256],"involved":[222],"MAPK":[224],"signaling":[225],"or":[226,235],"myeloid":[227],"leukemia":[228],"defined":[230],"KEGG":[233],"database,":[234],"known":[237,257],"physically":[239],"interact":[240],"each":[242],"other.":[243],"Additionally,":[244],"four":[245],"which":[249],"Hif1a,":[251],"Cebpb,":[252],"Nfkb1,":[253],"Atf1,":[255],"targets":[258],"rapamycin.":[260],"Furthermore,":[261],"trimmed":[263],"able":[266],"predict":[268],"Eno1":[269],"Hif1a;":[275],"this":[276],"could":[279],"not":[280],"detected":[282],"without":[283],"trimming":[284],"network.":[287],"CONCLUSIONS:":[288],"advantage":[290],"our":[292,302,329,350],"new":[293],"algorithm,":[294],"relative":[295],"NCA,":[299],"can":[304],"interactions.":[309],"Identifying":[310],"crucial":[316],"for":[317],"understanding":[318],"roles":[320],"pleiotropic":[322],"global":[323],"regulators,":[324],"p53.":[327],"Also,":[328],"overcome":[335],"NCA's":[336],"inability":[337],"analyze":[339],"large":[340],"networks":[341],"multiple":[343],"regulate":[345],"a":[346],"single":[347],"gene.":[348],"extends":[352],"applicability":[354],"NCA":[356],"realm":[359],"mammalian":[361]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":5}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
