{"id":"https://openalex.org/W2165342893","doi":"https://doi.org/10.1093/bioinformatics/btl231","title":"Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles","display_name":"Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles","publication_year":2006,"publication_date":"2006-07-15","ids":{"openalex":"https://openalex.org/W2165342893","doi":"https://doi.org/10.1093/bioinformatics/btl231","mag":"2165342893","pmid":"https://pubmed.ncbi.nlm.nih.gov/16873460"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl231","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl231","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069819603","display_name":"Elena J. Edelman","orcid":null},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elena Edelman","raw_affiliation_strings":["Computational Biology and Bioinformatics Program, Duke University 2 \u00a0 2 \u00a0 \u00a0 Durham NC 27708, USA","Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics Program, Duke University 2 \u00a0 2 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038843491","display_name":"Alessandro Porrello","orcid":null},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alessandro Porrello","raw_affiliation_strings":["Department of Medicine, Duke University 3 \u00a0 3 \u00a0 \u00a0 Durham NC 27708, USA","Department of Molecular Genetics and Microbiology, Duke University 4 \u00a0 4 \u00a0 \u00a0 Durham NC 27708, USA","Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA","Molecular Oncogenesis Laboratory, Regina Elena Cancer Institute 7 \u00a0 7 \u00a0 \u00a0 Via Delle Messi D'Oro 156, Rome, 00158, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Duke University 3 \u00a0 3 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Department of Molecular Genetics and Microbiology, Duke University 4 \u00a0 4 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Molecular Oncogenesis Laboratory, Regina Elena Cancer Institute 7 \u00a0 7 \u00a0 \u00a0 Via Delle Messi D'Oro 156, Rome, 00158, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080308005","display_name":"Justin Guinney","orcid":"https://orcid.org/0000-0003-1477-1888"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Justin Guinney","raw_affiliation_strings":["Computational Biology and Bioinformatics Program, Duke University 2 \u00a0 2 \u00a0 \u00a0 Durham NC 27708, USA","Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics Program, Duke University 2 \u00a0 2 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048741687","display_name":"Bala S. Balakumaran","orcid":null},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bala Balakumaran","raw_affiliation_strings":["Department of Medicine, Duke University 3 \u00a0 3 \u00a0 \u00a0 Durham NC 27708, USA","Department of Molecular Genetics and Microbiology, Duke University 4 \u00a0 4 \u00a0 \u00a0 Durham NC 27708, USA","Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Duke University 3 \u00a0 3 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Department of Molecular Genetics and Microbiology, Duke University 4 \u00a0 4 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101896600","display_name":"Andrea Bild","orcid":"https://orcid.org/0000-0003-4850-0453"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrea Bild","raw_affiliation_strings":["Department of Medicine, Duke University 3 \u00a0 3 \u00a0 \u00a0 Durham NC 27708, USA","Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Duke University 3 \u00a0 3 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058375967","display_name":"Phillip G. Febbo","orcid":"https://orcid.org/0000-0002-6496-4664"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Phillip G. Febbo","raw_affiliation_strings":["Department of Medicine, Duke University 3 \u00a0 3 \u00a0 \u00a0 Durham NC 27708, USA","Department of Molecular Genetics and Microbiology, Duke University 4 \u00a0 4 \u00a0 \u00a0 Durham NC 27708, USA","Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Duke University 3 \u00a0 3 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Department of Molecular Genetics and Microbiology, Duke University 4 \u00a0 4 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014241799","display_name":"Sayan Mukherjee","orcid":"https://orcid.org/0000-0002-6715-3920"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]},{"id":"https://openalex.org/I4210133369","display_name":"Decision Sciences (United States)","ror":"https://ror.org/03gcvf773","country_code":"US","type":"company","lineage":["https://openalex.org/I4210133369"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sayan Mukherjee","raw_affiliation_strings":["Department of Computer Science, Duke University 6 \u00a0 6 \u00a0 \u00a0 Durham NC 27708, USA","Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA","Institute of Statistics and Decision Sciences, Duke University 5 \u00a0 5 \u00a0 \u00a0 Durham NC 27708, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Duke University 6 \u00a0 6 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute for Genome Sciences & Policy, Duke University 1 \u00a0 1 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Institute of Statistics and Decision Sciences, Duke University 5 \u00a0 5 \u00a0 \u00a0 Durham NC 27708, USA","institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210133369"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5014241799"],"corresponding_institution_ids":["https://openalex.org/I170897317","https://openalex.org/I4210133369"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.3034,"has_fulltext":false,"cited_by_count":77,"citation_normalized_percentile":{"value":0.92602271,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"14","first_page":"e108","last_page":"e116"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.5593000054359436,"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":0.5593000054359436,"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":0.36410000920295715,"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":0.013799999840557575,"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/computational-biology","display_name":"Computational biology","score":0.6337558627128601},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5814699530601501},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.5672870874404907},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5565057396888733},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5262051224708557},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.49413421750068665},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4414345622062683},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4324020743370056},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.41837942600250244},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4162881374359131},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4115251302719116},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3711366355419159},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23161610960960388}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6337558627128601},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5814699530601501},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.5672870874404907},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5565057396888733},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5262051224708557},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.49413421750068665},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4414345622062683},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4324020743370056},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.41837942600250244},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4162881374359131},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4115251302719116},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3711366355419159},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23161610960960388},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D018401","descriptor_name":"Sample Size","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018401","descriptor_name":"Sample Size","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018401","descriptor_name":"Sample Size","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btl231","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl231","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16873460","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16873460","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.94.7582","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.94.7582","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.stat.duke.edu/~sayan/webPub/assess.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1480376833","https://openalex.org/W1504510381","https://openalex.org/W1523843467","https://openalex.org/W1554944419","https://openalex.org/W1571917377","https://openalex.org/W1580445772","https://openalex.org/W1969512609","https://openalex.org/W1988078905","https://openalex.org/W2058451329","https://openalex.org/W2059313996","https://openalex.org/W2088851040","https://openalex.org/W2102074241","https://openalex.org/W2109363337","https://openalex.org/W2111476798","https://openalex.org/W2121277505","https://openalex.org/W2123106337","https://openalex.org/W2130410032","https://openalex.org/W2136787567","https://openalex.org/W2139036189","https://openalex.org/W2148603752","https://openalex.org/W2150909545","https://openalex.org/W2151688340","https://openalex.org/W2158384363","https://openalex.org/W2164895949","https://openalex.org/W2314682596","https://openalex.org/W2408089991","https://openalex.org/W2751862591"],"related_works":["https://openalex.org/W2052655934","https://openalex.org/W104645380","https://openalex.org/W2027213253","https://openalex.org/W2017047508","https://openalex.org/W2165201120","https://openalex.org/W2023641020","https://openalex.org/W2188530857","https://openalex.org/W2133040682","https://openalex.org/W1971081588","https://openalex.org/W2041199873"],"abstract_inverted_index":{"MOTIVATION:":[0],"Gene":[1],"expression":[2,39,66,94,110,198],"profiling":[3],"experiments":[4],"in":[5,46,57,62,78,92,107,158,223],"cell":[6,133],"lines":[7],"and":[8,116,124,138,225],"animal":[9],"models":[10,199],"characterized":[11],"by":[12,24,72,171],"specific":[13,49],"genetic":[14],"or":[15],"molecular":[16,169],"perturbations":[17],"have":[18],"yielded":[19],"sets":[20,29,112,149],"of":[21,59,89,104,121,126,168,185,188,206,216],"genes":[22,61],"annotated":[23,71],"the":[25,87,101,122,159,166,183,203],"perturbation.":[26],"These":[27],"gene":[28,51,109,148],"can":[30,68,179,193,233],"serve":[31],"as":[32],"a":[33,43,48,81,152,214,228],"reference":[34,74],"base":[35],"for":[36,165,196],"interrogating":[37],"other":[38,117],"datasets.":[40,140],"For":[41],"example,":[42],"new":[44],"dataset":[45],"which":[47],"pathway":[50,105,143],"set":[52,64],"appears":[53],"to":[54,85,99],"be":[55,70,180,194,234],"enriched,":[56],"terms":[58],"multiple":[60],"that":[63,73,147,178],"evidencing":[65],"changes,":[67],"then":[69],"pathway.":[75],"We":[76,162],"introduce":[77],"this":[79],"paper":[80],"formal":[82],"statistical":[83],"method":[84,123],"measure":[86],"enrichment":[88,217],"each":[90],"sample":[91],"an":[93,175],"dataset.":[95],"This":[96,173],"allows":[97],"us":[98],"assay":[100],"natural":[102],"variation":[103],"activity":[106],"observed":[108],"data":[111,201],"from":[113,151],"clinical":[114],"cancer":[115,207],"studies.":[118],"RESULTS:":[119],"Validation":[120],"illustrations":[125],"biological":[127],"insights":[128],"gleaned":[129],"are":[130,155,208,221],"demonstrated":[131],"on":[132,202],"line":[134],"data,":[135],"mouse":[136],"models,":[137],"cancer-related":[139],"Using":[141],"oncogenic":[142],"signatures,":[144],"we":[145],"show":[146],"built":[150],"model":[153,160],"system":[154],"indeed":[156],"enriched":[157],"system.":[161],"employ":[163],"ASSESS":[164,192],"use":[167],"classification":[170],"pathways.":[172],"provides":[174],"accurate":[176],"classifier":[177],"interpreted":[181],"at":[182,236],"level":[184],"pathways":[186],"instead":[187],"individual":[189],"genes.":[190],"Finally,":[191],"used":[195],"cross-platform":[197],"where":[200],"same":[204],"type":[205],"integrated":[209],"over":[210],"different":[211],"platforms":[212],"into":[213],"space":[215],"scores.":[218],"AVAILABILITY:":[219],"Versions":[220],"available":[222],"Octave":[224],"Java":[226],"(with":[227],"graphical":[229],"user":[230],"interface).":[231],"Software":[232],"downloaded":[235],"http://people.genome.duke.edu/assess.":[237]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":6}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
