{"id":"https://openalex.org/W2059005938","doi":"https://doi.org/10.1186/1471-2105-15-79","title":"The characteristic direction: a geometrical approach to identify differentially expressed genes","display_name":"The characteristic direction: a geometrical approach to identify differentially expressed genes","publication_year":2014,"publication_date":"2014-03-20","ids":{"openalex":"https://openalex.org/W2059005938","doi":"https://doi.org/10.1186/1471-2105-15-79","mag":"2059005938","pmid":"https://pubmed.ncbi.nlm.nih.gov/24650281"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-79","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-79","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-79","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/10.1186/1471-2105-15-79","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068021572","display_name":"Neil R. Clark","orcid":"https://orcid.org/0000-0002-1844-0915"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Neil R Clark","raw_affiliation_strings":["Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017369402","display_name":"Kevin Hu","orcid":"https://orcid.org/0000-0001-7573-3880"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kevin S Hu","raw_affiliation_strings":["Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052691044","display_name":"Axel S. Feldmann","orcid":null},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Axel S Feldmann","raw_affiliation_strings":["Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100956507","display_name":"Yan Kou","orcid":null},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yan Kou","raw_affiliation_strings":["Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046028362","display_name":"Edward Y. Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward Y Chen","raw_affiliation_strings":["Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018902285","display_name":"Qiaonan Duan","orcid":null},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qiaonan Duan","raw_affiliation_strings":["Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY, 10029, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032951414","display_name":"Avi Ma\u2019ayan","orcid":"https://orcid.org/0000-0002-6904-1017"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Avi Ma\u2019ayan","raw_affiliation_strings":["Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pharmacology and Systems Therapeutics, Systems Biology Center New York (SBCNY), Icahn School of Medicine at Mount Sinai School, New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5068021572"],"corresponding_institution_ids":["https://openalex.org/I98704320"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":5.2644,"has_fulltext":true,"cited_by_count":211,"citation_normalized_percentile":{"value":0.96498818,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"15","issue":"1","first_page":"79","last_page":"79"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9182000160217285,"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":0.9182000160217285,"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":0.019099999219179153,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.016200000420212746,"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/dna-microarray","display_name":"DNA microarray","score":0.7615854144096375},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6766455173492432},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.5974954962730408},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5032927393913269},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.46676748991012573},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4237644672393799},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.396605521440506},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3681758642196655},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36365002393722534},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.31217461824417114}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.7615854144096375},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6766455173492432},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.5974954962730408},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5032927393913269},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.46676748991012573},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4237644672393799},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.396605521440506},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3681758642196655},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36365002393722534},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.31217461824417114}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-15-79","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-79","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-79","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:24650281","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24650281","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:europepmc.org:2991711","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC4000056","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:4000056","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4000056","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:10.1186/1471-2105-15-79","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-79","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-79","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/G1936110908","display_name":null,"funder_award_id":"P50GM071558","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2059005938.pdf","grobid_xml":"https://content.openalex.org/works/W2059005938.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W570304169","https://openalex.org/W1480376833","https://openalex.org/W1818591394","https://openalex.org/W1847694155","https://openalex.org/W1998902445","https://openalex.org/W2021129827","https://openalex.org/W2034269086","https://openalex.org/W2050159724","https://openalex.org/W2062649377","https://openalex.org/W2070050178","https://openalex.org/W2074414424","https://openalex.org/W2081098333","https://openalex.org/W2091735588","https://openalex.org/W2096919430","https://openalex.org/W2098023402","https://openalex.org/W2098792464","https://openalex.org/W2100079513","https://openalex.org/W2103017472","https://openalex.org/W2107018762","https://openalex.org/W2110891968","https://openalex.org/W2111063091","https://openalex.org/W2117692326","https://openalex.org/W2123106337","https://openalex.org/W2127293185","https://openalex.org/W2130410032","https://openalex.org/W2134582937","https://openalex.org/W2138003481","https://openalex.org/W2144227498","https://openalex.org/W2150414518","https://openalex.org/W2152239989","https://openalex.org/W2155423555","https://openalex.org/W2156631105","https://openalex.org/W2157795344","https://openalex.org/W2165909549","https://openalex.org/W2170140374","https://openalex.org/W2170146596","https://openalex.org/W2247766769","https://openalex.org/W2314203153","https://openalex.org/W4294107304"],"related_works":["https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W106077234","https://openalex.org/W2084813257","https://openalex.org/W2052655934","https://openalex.org/W2041374557","https://openalex.org/W2045929470","https://openalex.org/W2081929287","https://openalex.org/W2081127504","https://openalex.org/W2144348650"],"abstract_inverted_index":{"BACKGROUND:":[0],"Identifying":[1],"differentially":[2,251],"expressed":[3,252],"genes":[4,258],"(DEG)":[5],"is":[6,92,326],"a":[7,73,114],"fundamental":[8],"step":[9],"in":[10,63,102,174,240],"studies":[11],"that":[12,87,165,233,245,270,313],"perform":[13,279],"genome":[14],"wide":[15],"expression":[16,46,140,169],"profiling.":[17,68],"Typically,":[18],"DEG":[19,80,101,225,322],"are":[20,236,250,259],"identified":[21],"by":[22,261,318],"univariate":[23],"approaches":[24],"such":[25],"as":[26,130,132,159,161,201,203,213],"Significance":[27],"Analysis":[28],"of":[29,58,105,117,138,177,197,207,255,300],"Microarrays":[30],"(SAM)":[31],"or":[32,55],"Linear":[33],"Models":[34],"for":[35,39,66,99,184,217],"Microarray":[36],"Data":[37],"(LIMMA)":[38],"processing":[40],"cDNA":[41],"microarrays,":[42],"and":[43,109,147,170,253,293,343],"differential":[44],"gene":[45,168,281],"analysis":[47,57,291],"based":[48],"on":[49,309],"the":[50,82,88,103,123,154,186,198,208,222,243,248,256,262,271,288,294,301,319],"negative":[51],"binomial":[52],"distribution":[53],"(DESeq)":[54],"Empirical":[56],"Digital":[59],"Gene":[60,155],"Expression":[61,156],"data":[62,141,192],"R":[64],"(edgeR)":[65],"RNA-seq":[67],"RESULTS:":[69],"Here":[70],"we":[71,268],"present":[72],"new":[74,307],"geometrical":[75],"multivariate":[76],"approach":[77],"to":[78,238,278],"identify":[79],"called":[81],"Characteristic":[83,89,124,223,263,272,302],"Direction.":[84],"We":[85,120,231],"demonstrate":[86],"Direction":[90,125,224,264,273,303],"method":[91,126,187,227,304,325],"significantly":[93],"more":[94,254],"sensitive":[95],"than":[96],"existing":[97],"methods":[98],"identifying":[100,193],"context":[104],"transcription":[106],"factor":[107],"(TF)":[108],"drug":[110,148,205],"perturbation":[111],"responses":[112],"over":[113],"large":[115,136,179],"number":[116],"microarray":[118,139],"experiments.":[119],"also":[121],"benchmarked":[122],"using":[127,188,335],"synthetic":[128],"data,":[129],"well":[131,160,202],"RNA-Seq":[133,163],"data.":[134,190],"A":[135],"collection":[137],"from":[142,153],"TF":[143],"perturbations":[144,149],"(73":[145],"experiments)":[146,151],"(130":[150],"extracted":[152],"Omnibus":[157],"(GEO),":[158],"an":[162],"study":[164],"profiled":[166],"genome-wide":[167],"STAT3":[171],"DNA":[172,194],"binding":[173,195],"two":[175],"subtypes":[176],"diffuse":[178],"B-cell":[180],"Lymphoma,":[181],"were":[182,211],"used":[183,212,277],"benchmarking":[185],"real":[189],"ChIP-Seq":[191],"sites":[196],"perturbed":[199],"TFs,":[200],"known":[204],"targets":[206],"perturbing":[209],"drugs,":[210],"prior":[214],"knowledge":[215],"silver-standard":[216],"validation.":[218],"In":[219,266],"all":[220,345],"cases":[221],"calling":[226],"outperformed":[228],"other":[229],"methods.":[230,323],"find":[232],"when":[234,285],"drugs":[235],"applied":[237],"cells":[239],"various":[241,330],"contexts,":[242],"proteins":[244],"interact":[246],"with":[247,287],"drug-targets":[249],"corresponding":[257],"discovered":[260],"method.":[265],"addition,":[267],"show":[269],"conceptualization":[274],"can":[275],"be":[276],"improved":[280],"set":[282],"enrichment":[283,290],"analyses":[284],"compared":[286],"gene-set":[289],"(GSEA)":[292],"hypergeometric":[295],"test.":[296],"CONCLUSIONS:":[297],"The":[298,324],"application":[299],"may":[305],"shed":[306],"light":[308],"relevant":[310],"biological":[311],"mechanisms":[312],"would":[314],"have":[315],"remained":[316],"undiscovered":[317],"current":[320],"state-of-the-art":[321],"freely":[327],"accessible":[328],"via":[329],"open":[331],"source":[332],"code":[333],"implementations":[334],"four":[336],"popular":[337],"programming":[338],"languages:":[339],"R,":[340],"Python,":[341],"MATLAB":[342],"Mathematica,":[344],"available":[346],"at:":[347],"http://www.maayanlab.net/CD.":[348]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":22},{"year":2022,"cited_by_count":21},{"year":2021,"cited_by_count":33},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":25},{"year":2018,"cited_by_count":17},{"year":2017,"cited_by_count":11},{"year":2016,"cited_by_count":15},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}