{"id":"https://openalex.org/W2143423915","doi":"https://doi.org/10.1093/bioinformatics/bti394","title":"MADE4: an R package for multivariate analysis of gene expression data","display_name":"MADE4: an R package for multivariate analysis of gene expression data","publication_year":2005,"publication_date":"2005-03-29","ids":{"openalex":"https://openalex.org/W2143423915","doi":"https://doi.org/10.1093/bioinformatics/bti394","mag":"2143423915","pmid":"https://pubmed.ncbi.nlm.nih.gov/15797915"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti394","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2789/48971433/bioinformatics_21_11_2789.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2789/48971433/bioinformatics_21_11_2789.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082180580","display_name":"Aed\u00edn C. Culhane","orcid":"https://orcid.org/0000-0002-1395-9734"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"A. C. Culhane","raw_affiliation_strings":["Bioinformatics, Conway Institute, University College Dublin, Dublin 4, Ireland. aedin.culhane@ucd.ie","Bioinformatics, Conway Institute, University College Dublin  Dublin 4, Ireland"],"affiliations":[{"raw_affiliation_string":"Bioinformatics, Conway Institute, University College Dublin, Dublin 4, Ireland. aedin.culhane@ucd.ie","institution_ids":["https://openalex.org/I100930933"]},{"raw_affiliation_string":"Bioinformatics, Conway Institute, University College Dublin  Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045834199","display_name":"Jean Thioulouse","orcid":"https://orcid.org/0000-0001-7664-0598"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"J. Thioulouse","raw_affiliation_strings":["Laboratoire de Biomtrie et Biologie volutive, Universit Claude Bernard, Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France","Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, Universit\u00e9 Claude Bernard  Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Biomtrie et Biologie volutive, Universit Claude Bernard, Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France","institution_ids":["https://openalex.org/I100532134"]},{"raw_affiliation_string":"Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, Universit\u00e9 Claude Bernard  Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France","institution_ids":["https://openalex.org/I100532134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013133004","display_name":"Guy Perri\u00e8re","orcid":"https://orcid.org/0000-0002-6850-6265"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Universit\u00e9 Claude Bernard Lyon 1","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"G. Perriere","raw_affiliation_strings":["Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, Universit\u00e9 Claude Bernard  Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France"],"affiliations":[{"raw_affiliation_string":"Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, Universit\u00e9 Claude Bernard  Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France","institution_ids":["https://openalex.org/I100532134"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090607558","display_name":"Desmond G. Higgins","orcid":"https://orcid.org/0000-0002-3952-3285"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"D. G. Higgins","raw_affiliation_strings":["Bioinformatics, Conway Institute, University College Dublin, Dublin 4, Ireland and","Bioinformatics, Conway Institute, University College Dublin  Dublin 4, Ireland"],"affiliations":[{"raw_affiliation_string":"Bioinformatics, Conway Institute, University College Dublin, Dublin 4, Ireland and","institution_ids":["https://openalex.org/I100930933"]},{"raw_affiliation_string":"Bioinformatics, Conway Institute, University College Dublin  Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5082180580"],"corresponding_institution_ids":["https://openalex.org/I100930933"],"apc_list":null,"apc_paid":null,"fwci":3.5443,"has_fulltext":true,"cited_by_count":402,"citation_normalized_percentile":{"value":0.93348948,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"21","issue":"11","first_page":"2789","last_page":"2790"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9990000128746033,"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":0.9990000128746033,"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/T10594","display_name":"Genetic and phenotypic traits in livestock","score":0.9567000269889832,"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"}},{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.9560999870300293,"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/multivariate-statistics","display_name":"Multivariate statistics","score":0.7110158205032349},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6959884166717529},{"id":"https://openalex.org/keywords/multivariate-analysis","display_name":"Multivariate analysis","score":0.6267902851104736},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.520786464214325},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5086773037910461},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48461684584617615},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.43077677488327026},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3397948741912842},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29859402775764465},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2270757555961609},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1568392515182495},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.09205994009971619}],"concepts":[{"id":"https://openalex.org/C161584116","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate statistics","level":2,"score":0.7110158205032349},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6959884166717529},{"id":"https://openalex.org/C38180746","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate analysis","level":2,"score":0.6267902851104736},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.520786464214325},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5086773037910461},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48461684584617615},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.43077677488327026},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3397948741912842},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29859402775764465},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2270757555961609},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1568392515182495},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.09205994009971619}],"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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015999","descriptor_name":"Multivariate Analysis","qualifier_ui":null,"qualifier_name":null,"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":"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":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti394","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2789/48971433/bioinformatics_21_11_2789.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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:15797915","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15797915","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bti394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti394","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/11/2789/48971433/bioinformatics_21_11_2789.pdf","source":{"id":"https://openalex.org/S4210188263","display_name":"Computer applications in the biosciences","issn_l":"0266-7061","issn":["0266-7061","1460-2059"],"is_oa":false,"is_in_doaj":false,"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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2143423915.pdf","grobid_xml":"https://content.openalex.org/works/W2143423915.grobid-xml"},"referenced_works_count":8,"referenced_works":["https://openalex.org/W183117647","https://openalex.org/W1537484231","https://openalex.org/W1974948854","https://openalex.org/W2077085882","https://openalex.org/W2097553067","https://openalex.org/W2131666115","https://openalex.org/W2160697532","https://openalex.org/W2162491638"],"related_works":["https://openalex.org/W2406638334","https://openalex.org/W40745829","https://openalex.org/W4318262572","https://openalex.org/W1978357124","https://openalex.org/W1578824628","https://openalex.org/W2032728545","https://openalex.org/W1570805059","https://openalex.org/W4250754046","https://openalex.org/W4243682621","https://openalex.org/W2036849593"],"abstract_inverted_index":{"MADE4,":[0],"microarray":[1,12,45,64],"ade4,":[2,39],"is":[3],"a":[4,17],"software":[5],"package":[6,38],"that":[7,56],"facilitates":[8],"multivariate":[9,30,61],"analysis":[10,62],"of":[11,20,27,60,63],"gene-expression":[13,21],"data.":[14,46,65],"MADE4":[15,24,49],"accepts":[16],"wide":[18],"variety":[19],"data":[22],"formats.":[23],"takes":[25],"advantage":[26],"the":[28,36],"extensive":[29],"statistical":[31],"and":[32,53],"graphical":[33,52],"functions":[34],"in":[35,58],"R":[37],"extending":[40],"these":[41],"for":[42],"application":[43],"to":[44],"In":[47],"addition,":[48],"provides":[50],"new":[51],"visualization":[54],"tools":[55],"aid":[57],"interpretation":[59]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":20},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":21},{"year":2022,"cited_by_count":29},{"year":2021,"cited_by_count":30},{"year":2020,"cited_by_count":45},{"year":2019,"cited_by_count":27},{"year":2018,"cited_by_count":24},{"year":2017,"cited_by_count":24},{"year":2016,"cited_by_count":17},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":22}],"updated_date":"2026-04-01T17:29:45.350535","created_date":"2025-10-10T00:00:00"}