{"id":"https://openalex.org/W2060828805","doi":"https://doi.org/10.1186/1748-7188-4-7","title":"Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity","display_name":"Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity","publication_year":2009,"publication_date":"2009-04-22","ids":{"openalex":"https://openalex.org/W2060828805","doi":"https://doi.org/10.1186/1748-7188-4-7","mag":"2060828805","pmid":"https://pubmed.ncbi.nlm.nih.gov/19386098"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-4-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-4-7","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-4-7","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-4-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053208830","display_name":"Koji Kadota","orcid":"https://orcid.org/0000-0002-3907-4336"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Koji Kadota","raw_affiliation_strings":["Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. kadota@bi.a.u-tokyo.ac.jp","Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. kadota@bi.a.u-tokyo.ac.jp","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021966764","display_name":"Yuji Nakai","orcid":"https://orcid.org/0000-0002-2458-3875"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuji Nakai","raw_affiliation_strings":["Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan","Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102746753","display_name":"Kentaro Shimizu","orcid":"https://orcid.org/0000-0002-3245-0052"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kentaro Shimizu","raw_affiliation_strings":["Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan","Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053208830"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":4.0283,"has_fulltext":true,"cited_by_count":86,"citation_normalized_percentile":{"value":0.94688043,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"4","issue":"1","first_page":"7","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9546999931335449,"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":0.9546999931335449,"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":0.025800000876188278,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.0019000000320374966,"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/preprocessor","display_name":"Preprocessor","score":0.6593440771102905},{"id":"https://openalex.org/keywords/statistic","display_name":"Statistic","score":0.650391161441803},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.6386008858680725},{"id":"https://openalex.org/keywords/reproducibility","display_name":"Reproducibility","score":0.5753629207611084},{"id":"https://openalex.org/keywords/fold-change","display_name":"Fold change","score":0.5410656929016113},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.49057573080062866},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.46756061911582947},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4455453157424927},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4422876238822937},{"id":"https://openalex.org/keywords/receiver-operating-characteristic","display_name":"Receiver operating characteristic","score":0.4389646351337433},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.41692739725112915},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36720025539398193},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3640073537826538},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3324928283691406},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31868767738342285},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.26244106888771057},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20007464289665222},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18818378448486328}],"concepts":[{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.6593440771102905},{"id":"https://openalex.org/C89128539","wikidata":"https://www.wikidata.org/wiki/Q1949963","display_name":"Statistic","level":2,"score":0.650391161441803},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.6386008858680725},{"id":"https://openalex.org/C9893847","wikidata":"https://www.wikidata.org/wiki/Q1425625","display_name":"Reproducibility","level":2,"score":0.5753629207611084},{"id":"https://openalex.org/C2779018089","wikidata":"https://www.wikidata.org/wiki/Q17014303","display_name":"Fold change","level":4,"score":0.5410656929016113},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.49057573080062866},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.46756061911582947},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4455453157424927},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4422876238822937},{"id":"https://openalex.org/C58471807","wikidata":"https://www.wikidata.org/wiki/Q327120","display_name":"Receiver operating characteristic","level":2,"score":0.4389646351337433},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.41692739725112915},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36720025539398193},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3640073537826538},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3324928283691406},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31868767738342285},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.26244106888771057},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20007464289665222},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18818378448486328}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1748-7188-4-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-4-7","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-4-7","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:19386098","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19386098","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:a187e1d8a8d9417db55a62f21899e9bf","is_oa":false,"landing_page_url":"https://doaj.org/article/a187e1d8a8d9417db55a62f21899e9bf","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":"Algorithms for Molecular Biology, Vol 4, Iss 1, p 7 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2679019","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2679019","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":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-4-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-4-7","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-4-7","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3017878146","display_name":"Methods for detecting differentially expressed genes with reproducibility, sensitivity, and specificity from microarray data","funder_award_id":"21710208","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2060828805.pdf","grobid_xml":"https://content.openalex.org/works/W2060828805.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1570746489","https://openalex.org/W1967939830","https://openalex.org/W1973614663","https://openalex.org/W2000264668","https://openalex.org/W2002084527","https://openalex.org/W2010637767","https://openalex.org/W2013230094","https://openalex.org/W2031739742","https://openalex.org/W2035421116","https://openalex.org/W2038437697","https://openalex.org/W2076889248","https://openalex.org/W2081098333","https://openalex.org/W2098702528","https://openalex.org/W2109453886","https://openalex.org/W2111331733","https://openalex.org/W2114333898","https://openalex.org/W2116634113","https://openalex.org/W2119722989","https://openalex.org/W2120682915","https://openalex.org/W2122598723","https://openalex.org/W2130301347","https://openalex.org/W2144227498","https://openalex.org/W2146004021","https://openalex.org/W2146948904","https://openalex.org/W2154362705","https://openalex.org/W2157031069","https://openalex.org/W2157795344","https://openalex.org/W2158271999","https://openalex.org/W2160697532","https://openalex.org/W2162871532","https://openalex.org/W2170989872","https://openalex.org/W2172215633","https://openalex.org/W2582743722","https://openalex.org/W4294107304"],"related_works":["https://openalex.org/W2796636403","https://openalex.org/W2015700328","https://openalex.org/W2364565895","https://openalex.org/W2911678823","https://openalex.org/W2152648570","https://openalex.org/W2767847608","https://openalex.org/W3138028456","https://openalex.org/W2223549427","https://openalex.org/W1972696957","https://openalex.org/W2160802685"],"abstract_inverted_index":{"BACKGROUND:":[0],"To":[1],"identify":[2,57],"differentially":[3],"expressed":[4],"genes":[5,32,221],"(DEGs)":[6],"from":[7],"microarray":[8,277],"data,":[9,179],"users":[10],"of":[11,30,44,63,110,137,147,191,215,219,259,262,285,296],"the":[12,35,145,148,151,168,181,192,201,227,236,251,255,260,294],"Affymetrix":[13],"GeneChip":[14],"system":[15],"need":[16,280],"to":[17,23,33,56,70,76,270,281],"select":[18,282],"both":[19,161],"a":[20,28,45,60,158,212],"preprocessing":[21,46,125,263,286],"algorithm":[22,47],"obtain":[24,34],"expression-level":[25],"measurements":[26],"and":[27,48,65,117,133,163,177,180,209,242,274,288],"way":[29],"ranking":[31,50,89,204,290],"most":[36],"plausible":[37],"candidates.":[38],"We":[39,83,165,292],"recently":[40],"recommended":[41],"suitable":[42,283],"combinations":[43,79,284],"gene":[49,203,289],"method":[51,170,183],"that":[52,167,200,269],"can":[53],"be":[54],"used":[55],"DEGs":[58],"with":[59,123],"higher":[61,213,231],"level":[62,214],"sensitivity":[64,162],"specificity.":[66,164],"However,":[67],"in":[68,276,299],"addition":[69],"these":[71],"recommendations,":[72],"researchers":[73],"also":[74],"want":[75],"know":[77],"which":[78],"enhance":[80],"reproducibility.":[81],"RESULTS:":[82],"compared":[84],"eight":[85],"conventional":[86],"methods":[87,205,229,238,257],"for":[88,160,173,186,226,235,248],"genes:":[90],"weighted":[91],"average":[92,95],"difference":[93,96],"(WAD),":[94],"(AD),":[97],"fold":[98],"change":[99],"(FC),":[100],"rank":[101],"products":[102],"(RP),":[103],"moderated":[104,119],"t":[105,114,120],"statistic":[106,115,121],"(modT),":[107],"significance":[108],"analysis":[109,190],"microarrays":[111],"(samT),":[112],"shrinkage":[113],"(shrinkT),":[116],"intensity-based":[118],"(ibmT)":[122],"six":[124],"algorithms":[126,287],"(PLIER,":[127],"VSN,":[128],"FARMS,":[129],"multi-mgMOS":[130],"(mmgMOS),":[131],"MBEI,":[132],"GCRMA).":[134],"A":[135],"total":[136],"36":[138],"real":[139],"experimental":[140],"datasets":[141,198],"was":[142],"evaluated":[143],"on":[144],"basis":[146],"area":[149],"under":[150],"receiver":[152],"operating":[153],"characteristic":[154],"curve":[155],"(AUC)":[156],"as":[157],"measure":[159],"found":[166],"RP":[169,301],"performed":[171,184],"well":[172,185],"VSN-,":[174],"FARMS-,":[175],"MBEI-,":[176],"GCRMA-preprocessed":[178],"WAD":[182,249],"mmgMOS-preprocessed":[187],"data.":[188],"Our":[189,266],"MicroArray":[193],"Quality":[194],"Control":[195],"(MAQC)":[196],"project's":[197],"showed":[199],"FC-based":[202,228,256,297],"(WAD,":[206],"AD,":[207],"FC,":[208],"RP)":[210],"had":[211],"reproducibility:":[216],"The":[217],"percentages":[218],"overlapping":[220],"(POGs)":[222],"across":[223],"different":[224],"sites":[225],"were":[230,250],"overall":[232,253],"than":[233],"those":[234],"t-statistic-based":[237],"(modT,":[239],"samT,":[240],"shrinkT,":[241],"ibmT).":[243],"In":[244],"particular,":[245],"POG":[246],"values":[247],"highest":[252],"among":[254],"irrespective":[258],"choice":[261],"algorithm.":[264],"CONCLUSION:":[265],"results":[267],"demonstrate":[268],"increase":[271],"sensitivity,":[272],"specificity,":[273],"reproducibility":[275],"analyses,":[278],"we":[279],"methods.":[291],"recommend":[293],"use":[295],"methods,":[298],"particular":[300],"or":[302],"WAD.":[303]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":9},{"year":2013,"cited_by_count":9},{"year":2012,"cited_by_count":7}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
