{"id":"https://openalex.org/W2120803941","doi":"https://doi.org/10.1186/1471-2105-8-347","title":"A unified framework for finding differentially expressed genes from microarray experiments","display_name":"A unified framework for finding differentially expressed genes from microarray experiments","publication_year":2007,"publication_date":"2007-09-18","ids":{"openalex":"https://openalex.org/W2120803941","doi":"https://doi.org/10.1186/1471-2105-8-347","mag":"2120803941","pmid":"https://pubmed.ncbi.nlm.nih.gov/17877806"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-347","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-347","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-347","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/10.1186/1471-2105-8-347","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052958888","display_name":"Jahangheer Shaik","orcid":"https://orcid.org/0000-0001-5509-6570"},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jahangheer S Shaik","raw_affiliation_strings":["Department of Electrical and Computer Engineering, CVPIA Lab, University of Memphis, Memphis, TN-38152, USA. jshaik@memphis.edu","Department of Electrical and Computer Engineering, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, CVPIA Lab, University of Memphis, Memphis, TN-38152, USA. jshaik@memphis.edu","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069645522","display_name":"Mohammed Yeasin","orcid":"https://orcid.org/0000-0003-0579-3030"},"institutions":[{"id":"https://openalex.org/I94658018","display_name":"University of Memphis","ror":"https://ror.org/01cq23130","country_code":"US","type":"education","lineage":["https://openalex.org/I94658018"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mohammed Yeasin","raw_affiliation_strings":["4Center for Advanced Robotics, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA","Bioinformatics Program, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA","Biomedical Engineering, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA","Department of Electrical and Computer Engineering, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA","Software Testing and Excellence Program University of Memphis, Memphis, TN, 38152, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4Center for Advanced Robotics, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Bioinformatics Program, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Biomedical Engineering, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Department of Electrical and Computer Engineering, CVPIA Lab, University of Memphis, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]},{"raw_affiliation_string":"Software Testing and Excellence Program University of Memphis, Memphis, TN, 38152, USA","institution_ids":["https://openalex.org/I94658018"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5069645522"],"corresponding_institution_ids":["https://openalex.org/I94658018"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.1992,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.77947455,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"8","issue":"1","first_page":"347","last_page":"347"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9602000117301941,"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":0.9602000117301941,"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":0.026200000196695328,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.0012000000569969416,"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/dna-microarray","display_name":"DNA microarray","score":0.7351598739624023},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.646007776260376},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6316093802452087},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5397208333015442},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.5324434041976929},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5076678991317749},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4385165572166443},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4277167320251465},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3392925262451172},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3390360176563263},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2875315845012665}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.7351598739624023},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.646007776260376},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6316093802452087},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5397208333015442},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.5324434041976929},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5076678991317749},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4385165572166443},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4277167320251465},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3392925262451172},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3390360176563263},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2875315845012665}],"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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","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},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-8-347","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-347","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-347","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:17877806","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17877806","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:doaj.org/article:b544354a4f934cd5a19042af7d373bc1","is_oa":false,"landing_page_url":"https://doaj.org/article/b544354a4f934cd5a19042af7d373bc1","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 8, Iss 1, p 347 (2007)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2099446","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2099446","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:10.1186/1471-2105-8-347","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-347","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-347","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":[],"funders":[{"id":"https://openalex.org/F4320312842","display_name":"University of Memphis","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120803941.pdf","grobid_xml":"https://content.openalex.org/works/W2120803941.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W410991710","https://openalex.org/W648027589","https://openalex.org/W1490760466","https://openalex.org/W1498486940","https://openalex.org/W1596515083","https://openalex.org/W1964895626","https://openalex.org/W2001619934","https://openalex.org/W2027514721","https://openalex.org/W2051224630","https://openalex.org/W2087684630","https://openalex.org/W2093463665","https://openalex.org/W2097557760","https://openalex.org/W2100691497","https://openalex.org/W2105793531","https://openalex.org/W2106227366","https://openalex.org/W2107598685","https://openalex.org/W2109363337","https://openalex.org/W2109986840","https://openalex.org/W2110065044","https://openalex.org/W2111203738","https://openalex.org/W2115617081","https://openalex.org/W2116821545","https://openalex.org/W2124597839","https://openalex.org/W2135000328","https://openalex.org/W2135187880","https://openalex.org/W2140942285","https://openalex.org/W2142231242","https://openalex.org/W2144792853","https://openalex.org/W2150926065","https://openalex.org/W2152012752","https://openalex.org/W2157795344","https://openalex.org/W2483904106","https://openalex.org/W2799002609","https://openalex.org/W2799061466","https://openalex.org/W2906942290","https://openalex.org/W4206021096","https://openalex.org/W4211107039","https://openalex.org/W4244494905","https://openalex.org/W4244638854","https://openalex.org/W4285719527","https://openalex.org/W4294107304"],"related_works":["https://openalex.org/W1996185163","https://openalex.org/W170658859","https://openalex.org/W2081127504","https://openalex.org/W1483316219","https://openalex.org/W4310366902","https://openalex.org/W3023720143","https://openalex.org/W2183420549","https://openalex.org/W2490137852","https://openalex.org/W2039699813","https://openalex.org/W2081507994"],"abstract_inverted_index":{"BACKGROUND:":[0],"This":[1,266],"paper":[2,267],"presents":[3,268],"a":[4,142,229,269],"unified":[5,104,154,161,204,270,397,421],"framework":[6,19,105,162,205,271,422],"for":[7,236,272],"finding":[8],"differentially":[9,430],"expressed":[10,431],"genes":[11,31,277,321,340,432],"(DEGs)":[12],"from":[13,278,433],"the":[14,54,60,70,76,85,96,102,119,123,135,138,149,153,160,200,203,207,223,237,243,255,258,273,279,298,308,317,348,351,365,368,378,381,395,420],"microarray":[15,192,263,285,362,385,406,434],"data.":[16,435],"The":[17,35,56,80,88,99,157,185,302,331,371,392],"proposed":[18,103,259,369,382,396],"has":[20],"three":[21,92,411],"interrelated":[22],"modules:":[23],"(i)":[24],"gene":[25,40,61,107,328,425],"ranking,":[26],"ii)":[27],"significance":[28],"analysis":[29,244,314],"of":[30,73,95,101,122,159,174,202,248,257,276,300,304,310,319,339,350,367,380,390,394,413],"and":[32,47,68,137,182,218,312,345,359],"(iii)":[33],"validation.":[34],"first":[36,110],"module":[37,58,90,293],"uses":[38],"two":[39,71,196,388,403],"selection":[41,108,275,299,338,426],"algorithms,":[42],"namely,":[43,335],"a)":[44],"two-way":[45],"clustering":[46,132],"b)":[48],"combined":[49],"adaptive":[50,130],"ranking":[51,167,289,329],"to":[52,147,253,261,306,399],"rank":[53],"genes.":[55,301],"second":[57],"converts":[59],"ranks":[62,305],"into":[63],"p-values":[64,74,311],"using":[65,75,84,112,152,189,341,410],"an":[66,129],"R-test":[67],"fuses":[69],"sets":[72,247,412],"Fisher's":[77],"omnibus":[78],"criterion.":[79],"DEGs":[81,124,150],"are":[82],"selected":[83],"FDR":[86,313,342],"analysis.":[87,116],"third":[89],"performs":[91],"fold":[93,231,333],"validations":[94],"obtained":[97,151,188],"DEGs.":[98,352],"robustness":[100,336],"in":[106,226,292,297,316,337,428],"is":[109,125,145,163,234,251,408],"illustrated":[111],"false":[113],"discovery":[114],"rate":[115],"In":[117,241],"addition,":[118,242],"clustering-based":[120],"validation":[121,232],"performed":[126,146,252],"by":[127],"employing":[128],"subspace-based":[131],"algorithm":[133],"on":[134,213,245,327,355,373,384],"training":[136],"test":[139],"datasets.":[140,240,264],"Finally,":[141],"projection-based":[143],"visualization":[144,346],"validate":[148],"framework.":[155],"RESULTS:":[156],"performance":[158,186],"compared":[164],"with":[165,387],"well-known":[166],"algorithms":[168],"such":[169],"as":[170,281,283],"t-statistics,":[171],"Significance":[172],"Analysis":[173],"Microarrays":[175],"(SAM),":[176],"Adaptive":[177,180],"Ranking,":[178],"Combined":[179],"Ranking":[181],"Two-way":[183],"Clustering.":[184],"curves":[187],"50":[190,356],"simulated":[191],"datasets":[193,217,221,358,363,376,386,407],"each":[194],"following":[195],"different":[197,288],"distributions":[198],"indicate":[199],"superiority":[201],"over":[206],"other":[208,424],"reported":[209],"algorithms.":[210],"Further":[211],"analyses":[212,354,372,417],"3":[214,219,230,246,332,374],"real":[215,361],"cancer":[216,239,375],"Parkinson's":[220,249,414],"show":[222,418],"similar":[224],"improvement":[225],"performance.":[227],"First,":[228],"process":[233],"provided":[235],"two-sample":[238,280],"data":[250],"demonstrate":[254,347,377],"scalability":[256,393],"method":[260],"multi-sample":[262,284,400],"CONCLUSION:":[265],"robust":[274],"well":[282],"experiments.":[286],"Two":[287],"methods":[290,427],"used":[291],"1":[294],"bring":[295],"diversity":[296],"conversion":[303],"p-values,":[307],"fusion":[309],"aid":[315],"identification":[318],"significant":[320],"which":[322],"cannot":[323],"be":[324],"judged":[325],"based":[326],"alone.":[330],"validation,":[334],"analysis,":[343],"clustering,":[344],"relevance":[349],"Empirical":[353,416],"artificial":[357],"6":[360],"illustrate":[364],"efficacy":[366],"approach.":[370],"utility":[379],"approach":[383,398],"classes":[389],"samples.":[391],"(more":[401],"than":[402],"sample":[404],"classes)":[405],"addressed":[409],"Data.":[415],"that":[419],"outperformed":[423],"selecting":[429]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}