{"id":"https://openalex.org/W2807134042","doi":"https://doi.org/10.1186/s13040-018-0166-8","title":"Gene set analysis methods: a systematic comparison","display_name":"Gene set analysis methods: a systematic comparison","publication_year":2018,"publication_date":"2018-05-31","ids":{"openalex":"https://openalex.org/W2807134042","doi":"https://doi.org/10.1186/s13040-018-0166-8","mag":"2807134042","pmid":"https://pubmed.ncbi.nlm.nih.gov/29881462"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-018-0166-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-018-0166-8","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-018-0166-8","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-018-0166-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045647597","display_name":"Ravi Mathur","orcid":"https://orcid.org/0000-0001-6785-0032"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]},{"id":"https://openalex.org/I180297670","display_name":"RTI International","ror":"https://ror.org/052tfza37","country_code":"US","type":"funder","lineage":["https://openalex.org/I180297670"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ravi Mathur","raw_affiliation_strings":["1Bioinformatics Research Center, North Carolina State University, Raleigh, NC USA","2Department of Statistics, North Carolina State University, Raleigh, NC USA","4Present address: RTI International, Research Triangle Park, Durham, NC USA","Department of Statistics, North Carolina State University, Raleigh, NC, USA","Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","Present address: RTI International, Research Triangle Park, Durham, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Bioinformatics Research Center, North Carolina State University, Raleigh, NC USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"2Department of Statistics, North Carolina State University, Raleigh, NC USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"4Present address: RTI International, Research Triangle Park, Durham, NC USA","institution_ids":["https://openalex.org/I180297670"]},{"raw_affiliation_string":"Department of Statistics, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Present address: RTI International, Research Triangle Park, Durham, NC, USA","institution_ids":["https://openalex.org/I180297670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064332538","display_name":"Daniel M. Rotroff","orcid":"https://orcid.org/0000-0003-0553-3220"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Rotroff","raw_affiliation_strings":["1Bioinformatics Research Center, North Carolina State University, Raleigh, NC USA","2Department of Statistics, North Carolina State University, Raleigh, NC USA","Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","Department of Statistics, North Carolina State University, Raleigh, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Bioinformatics Research Center, North Carolina State University, Raleigh, NC USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"2Department of Statistics, North Carolina State University, Raleigh, NC USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Department of Statistics, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101542954","display_name":"Jun Ma","orcid":"https://orcid.org/0000-0003-4354-2523"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Ma","raw_affiliation_strings":["1Bioinformatics Research Center, North Carolina State University, Raleigh, NC USA","2Department of Statistics, North Carolina State University, Raleigh, NC USA","Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","Department of Statistics, North Carolina State University, Raleigh, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1Bioinformatics Research Center, North Carolina State University, Raleigh, NC USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"2Department of Statistics, North Carolina State University, Raleigh, NC USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Department of Statistics, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060606663","display_name":"Ali Shojaie","orcid":"https://orcid.org/0000-0001-8846-3533"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210101190","display_name":"Cancer Research And Biostatistics","ror":"https://ror.org/01575p865","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210101190"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ali Shojaie","raw_affiliation_strings":["3Department of Biostatistics, University of Washington, Seattle, WA USA","Department of Biostatistics, University of Washington, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3Department of Biostatistics, University of Washington, Seattle, WA USA","institution_ids":["https://openalex.org/I201448701","https://openalex.org/I4210101190"]},{"raw_affiliation_string":"Department of Biostatistics, University of Washington, Seattle, WA, USA","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055785853","display_name":"Alison A. Motsinger\u2010Reif","orcid":"https://orcid.org/0000-0003-1346-2493"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alison Motsinger-Reif","raw_affiliation_strings":["1Bioinformatics Research Center, North Carolina State University, Raleigh, NC USA","2Department of Statistics, North Carolina State University, Raleigh, NC USA","Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","Department of Statistics, North Carolina State University, Raleigh, NC, USA"],"raw_orcid":"https://orcid.org/0000-0003-1346-2493","affiliations":[{"raw_affiliation_string":"1Bioinformatics Research Center, North Carolina State University, Raleigh, NC USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"2Department of Statistics, North Carolina State University, Raleigh, NC USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Department of Statistics, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5055785853"],"corresponding_institution_ids":["https://openalex.org/I137902535"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.6983,"has_fulltext":true,"cited_by_count":99,"citation_normalized_percentile":{"value":0.94313293,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"11","issue":"1","first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7713000178337097,"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":0.7713000178337097,"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/T10885","display_name":"Gene expression and cancer classification","score":0.08569999784231186,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.025699999183416367,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/computer-science","display_name":"Computer science","score":0.6356271505355835},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.592658519744873},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.430486798286438},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4270959198474884},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3680110275745392},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.36635327339172363},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16699424386024475},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08452245593070984}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6356271505355835},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.592658519744873},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.430486798286438},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4270959198474884},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3680110275745392},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.36635327339172363},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16699424386024475},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08452245593070984}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13040-018-0166-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-018-0166-8","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-018-0166-8","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:29881462","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29881462","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":"BioData mining","raw_type":null},{"id":"pmh:oai:doaj.org/article:bd6680547fec402d8eb2d4ccbc856f8d","is_oa":true,"landing_page_url":"https://doaj.org/article/bd6680547fec402d8eb2d4ccbc856f8d","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 11, Iss 1, Pp 1-19 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4945557","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5984476","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5984476","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5984476","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":"BioData Min","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13040-018-0166-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-018-0166-8","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-018-0166-8","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3080013420","display_name":null,"funder_award_id":"P01 CA142538","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3362432313","display_name":null,"funder_award_id":"P01 CA142538","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3745116027","display_name":null,"funder_award_id":"R01 GM114029","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5435571204","display_name":null,"funder_award_id":"R01 CA161608","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6236946409","display_name":null,"funder_award_id":"5R01CA161608","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G74368922","display_name":null,"funder_award_id":"K01 HL124050","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7646514433","display_name":null,"funder_award_id":"R01 HL110380","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"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/W2807134042.pdf","grobid_xml":"https://content.openalex.org/works/W2807134042.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1968005447","https://openalex.org/W1978337436","https://openalex.org/W1983463159","https://openalex.org/W1984065010","https://openalex.org/W1996913705","https://openalex.org/W2008895037","https://openalex.org/W2010541165","https://openalex.org/W2012150214","https://openalex.org/W2026785345","https://openalex.org/W2027895157","https://openalex.org/W2047190758","https://openalex.org/W2061554433","https://openalex.org/W2100980426","https://openalex.org/W2101536220","https://openalex.org/W2103017472","https://openalex.org/W2106840507","https://openalex.org/W2109972881","https://openalex.org/W2110065044","https://openalex.org/W2110687686","https://openalex.org/W2112220625","https://openalex.org/W2116634113","https://openalex.org/W2117692326","https://openalex.org/W2118258530","https://openalex.org/W2119454933","https://openalex.org/W2120118929","https://openalex.org/W2120865735","https://openalex.org/W2121604817","https://openalex.org/W2122630333","https://openalex.org/W2125951903","https://openalex.org/W2127551600","https://openalex.org/W2128601422","https://openalex.org/W2130410032","https://openalex.org/W2131848047","https://openalex.org/W2132105963","https://openalex.org/W2134736660","https://openalex.org/W2139036189","https://openalex.org/W2146512944","https://openalex.org/W2148708580","https://openalex.org/W2154431984","https://openalex.org/W2167119716","https://openalex.org/W2167778120","https://openalex.org/W2170989872","https://openalex.org/W2190430946","https://openalex.org/W2235443461","https://openalex.org/W2237297286","https://openalex.org/W2339774221","https://openalex.org/W2346501107","https://openalex.org/W2423170580","https://openalex.org/W2461625475","https://openalex.org/W2516667533","https://openalex.org/W2963190765","https://openalex.org/W4230770774","https://openalex.org/W6606281016"],"related_works":["https://openalex.org/W4234711916","https://openalex.org/W2027108423","https://openalex.org/W1855666948","https://openalex.org/W2758561209","https://openalex.org/W1548095260","https://openalex.org/W2343361478","https://openalex.org/W2594414941","https://openalex.org/W2781711915","https://openalex.org/W2112817590","https://openalex.org/W1555291398"],"abstract_inverted_index":{"BACKGROUND:":[0],"Gene":[1,77,118],"set":[2,30,78,112,140,198],"analysis":[3,31,113,141,199],"is":[4,21,102,204],"a":[5,53,86],"valuable":[6],"tool":[7],"to":[8,62,194],"summarize":[9],"high-dimensional":[10],"gene":[11,29,111,139,146,197],"expression":[12],"data":[13,83],"in":[14,45,60],"terms":[15],"of":[16,25,110,125,171,175,188,196],"biologically":[17],"relevant":[18],"sets.":[19],"This":[20],"an":[22],"active":[23],"area":[24],"research":[26],"and":[27,64,93,107,127,131,157,161,177],"numerous":[28],"methods":[32,114,142,176,210],"have":[33,42],"been":[34,43],"developed.":[35],"Despite":[36],"this":[37,49,189],"popularity,":[38],"systematic":[39],"comparative":[40],"studies":[41],"limited":[44],"scope.":[46],"METHODS:":[47],"In":[48],"study":[50,56,190],"we":[51],"present":[52],"semi-synthetic":[54],"simulation":[55],"using":[57,145],"real":[58],"datasets":[59,106],"order":[61],"test":[63],"compare":[65],"commonly":[66],"used":[67],"methods.":[68,137,200],"RESULTS:":[69],"A":[70],"software":[71,101,203],"pipeline,":[72],"Flexible":[73],"Algorithm":[74],"for":[75,117,163,168,206,208],"Novel":[76],"Simulation":[79],"(FANGS)":[80],"develops":[81],"simulated":[82],"based":[84],"on":[85],"prostate":[87],"cancer":[88],"dataset":[89],"where":[90],"the":[91,149,169,172],"KRAS":[92],"TGF-\u03b2":[94],"pathways":[95],"were":[96],"differentially":[97],"expressed.":[98],"The":[99,153,186,201],"FANGS":[100,202],"compatible":[103],"with":[104],"other":[105],"pathways.":[108],"Comparisons":[109],"are":[115,143,159,166],"presented":[116,162],"Set":[119],"Enrichment":[120],"Analysis":[121,124],"(GSEA),":[122],"Significance":[123],"Function":[126],"Expression":[128],"(SAFE),":[129],"sigPathway,":[130],"Correlation":[132],"Adjusted":[133],"Mean":[134],"RAnk":[135],"(CAMERA)":[136],"All":[138],"tested":[144],"sets":[147],"from":[148],"MSigDB":[150],"knowledge":[151],"base.":[152],"false":[154],"positive":[155],"rate":[156],"power":[158],"estimated":[160],"comparison.":[164],"Recommendations":[165],"made":[167],"utility":[170],"default":[173],"settings":[174],"each":[178],"method's":[179],"sensitivity":[180],"towards":[181],"various":[182],"effect":[183],"sizes.":[184],"CONCLUSIONS:":[185],"results":[187],"provide":[191],"empirical":[192],"guidance":[193],"users":[195],"available":[205],"researchers":[207],"continued":[209],"comparisons.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":9},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":2}],"updated_date":"2026-07-03T08:13:44.112507","created_date":"2025-10-10T00:00:00"}