{"id":"https://openalex.org/W2126926732","doi":"https://doi.org/10.1109/icme.2003.1221348","title":"Interactive color mosaic and dendrogram displays for signal/noise optimization in microarray data analysis","display_name":"Interactive color mosaic and dendrogram displays for signal/noise optimization in microarray data analysis","publication_year":2003,"publication_date":"2003-01-01","ids":{"openalex":"https://openalex.org/W2126926732","doi":"https://doi.org/10.1109/icme.2003.1221348","mag":"2126926732"},"language":"en","primary_location":{"id":"doi:10.1109/icme.2003.1221348","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icme.2003.1221348","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2003 International Conference on Multimedia and Expo. ICME '03. Proceedings (Cat. No.03TH8698)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://scholarworks.umass.edu/cgi/viewcontent.cgi?article=1133&context=cs_faculty_pubs","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012388103","display_name":"Jinwook Seo","orcid":"https://orcid.org/0000-0002-7734-822X"},"institutions":[{"id":"https://openalex.org/I4210142372","display_name":"Human Media","ror":"https://ror.org/04072nk43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210142372"]},{"id":"https://openalex.org/I1336742384","display_name":"Children's National","ror":"https://ror.org/03wa2q724","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1336742384"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jinwook Seo","raw_affiliation_strings":["Department of Computer Science & Human-Computer Interaction Laboratory, University of Maryland, USA","Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Human-Computer Interaction Laboratory, University of Maryland, USA","institution_ids":["https://openalex.org/I4210142372"]},{"raw_affiliation_string":"Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA","institution_ids":["https://openalex.org/I1336742384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032535946","display_name":"Marina Bakay","orcid":null},"institutions":[{"id":"https://openalex.org/I1336742384","display_name":"Children's National","ror":"https://ror.org/03wa2q724","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1336742384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. Bakay","raw_affiliation_strings":["Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA"],"affiliations":[{"raw_affiliation_string":"Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA","institution_ids":["https://openalex.org/I1336742384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032679283","display_name":"Po Zhao","orcid":"https://orcid.org/0000-0001-7362-7670"},"institutions":[{"id":"https://openalex.org/I1336742384","display_name":"Children's National","ror":"https://ror.org/03wa2q724","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1336742384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Po Zhao","raw_affiliation_strings":["Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA"],"affiliations":[{"raw_affiliation_string":"Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA","institution_ids":["https://openalex.org/I1336742384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101922813","display_name":"Yi-Wen Chen","orcid":"https://orcid.org/0000-0002-5886-1714"},"institutions":[{"id":"https://openalex.org/I1336742384","display_name":"Children's National","ror":"https://ror.org/03wa2q724","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1336742384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yi-Wen Chen","raw_affiliation_strings":["Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA"],"affiliations":[{"raw_affiliation_string":"Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA","institution_ids":["https://openalex.org/I1336742384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110121969","display_name":"P. M. Clarkson","orcid":null},"institutions":[{"id":"https://openalex.org/I24603500","display_name":"University of Massachusetts Amherst","ror":"https://ror.org/0072zz521","country_code":"US","type":"education","lineage":["https://openalex.org/I24603500"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"P. Clarkson","raw_affiliation_strings":["Exercise Science, University of Massachusetts, Amherst, USA"],"affiliations":[{"raw_affiliation_string":"Exercise Science, University of Massachusetts, Amherst, USA","institution_ids":["https://openalex.org/I24603500"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111618153","display_name":"B. Shneiderman","orcid":null},"institutions":[{"id":"https://openalex.org/I4210142372","display_name":"Human Media","ror":"https://ror.org/04072nk43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210142372"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. Shneiderman","raw_affiliation_strings":["Department of Computer Science & Human-Computer Interaction Laboratory, University of Maryland, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science & Human-Computer Interaction Laboratory, University of Maryland, USA","institution_ids":["https://openalex.org/I4210142372"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086088688","display_name":"Eric P. Hoffman","orcid":"https://orcid.org/0000-0001-6470-5139"},"institutions":[{"id":"https://openalex.org/I1336742384","display_name":"Children's National","ror":"https://ror.org/03wa2q724","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1336742384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E.P. Hoffman","raw_affiliation_strings":["Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA"],"affiliations":[{"raw_affiliation_string":"Research Center for Genetic Medicine, Children''s Hospital National Medical Center, USA","institution_ids":["https://openalex.org/I1336742384"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5012388103"],"corresponding_institution_ids":["https://openalex.org/I1336742384","https://openalex.org/I4210142372"],"apc_list":null,"apc_paid":null,"fwci":1.487,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.81377915,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"III","last_page":"461"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9994000196456909,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/cluster-analysis","display_name":"Cluster analysis","score":0.7484359741210938},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6917743682861328},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.6735520362854004},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5759467482566833},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5686413049697876},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5575011372566223},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.5090886950492859},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4511104226112366},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.14101433753967285}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7484359741210938},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6917743682861328},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.6735520362854004},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5759467482566833},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5686413049697876},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5575011372566223},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.5090886950492859},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4511104226112366},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.14101433753967285}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/icme.2003.1221348","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icme.2003.1221348","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2003 International Conference on Multimedia and Expo. ICME '03. Proceedings (Cat. No.03TH8698)","raw_type":"proceedings-article"},{"id":"pmh:oai:scholarworks.umass.edu:cs_faculty_pubs-1133","is_oa":true,"landing_page_url":"https://scholarworks.umass.edu/cs_faculty_pubs/134","pdf_url":"https://scholarworks.umass.edu/cgi/viewcontent.cgi?article=1133&context=cs_faculty_pubs","source":{"id":"https://openalex.org/S4306402240","display_name":"ScholarWorks@UMassAmherst (University of Massachusetts Amherst)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I24603500","host_organization_name":"University of Massachusetts Amherst","host_organization_lineage":["https://openalex.org/I24603500"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Science Department Faculty Publication Series","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.881.9886","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.881.9886","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://scholarworks.umass.edu/cgi/viewcontent.cgi?article%3D1133%26context%3Dcs_faculty_pubs","raw_type":"text"},{"id":"pmh:oai:scholarworks.umass.edu:20.500.14394/9761","is_oa":false,"landing_page_url":"https://hdl.handle.net/20.500.14394/9761","pdf_url":null,"source":{"id":"https://openalex.org/S4306402057","display_name":"Scholarworks (University of Massachusetts Amherst)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I24603500","host_organization_name":"University of Massachusetts Amherst","host_organization_lineage":["https://openalex.org/I24603500"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"published","raw_type":"Article"}],"best_oa_location":{"id":"pmh:oai:scholarworks.umass.edu:cs_faculty_pubs-1133","is_oa":true,"landing_page_url":"https://scholarworks.umass.edu/cs_faculty_pubs/134","pdf_url":"https://scholarworks.umass.edu/cgi/viewcontent.cgi?article=1133&context=cs_faculty_pubs","source":{"id":"https://openalex.org/S4306402240","display_name":"ScholarWorks@UMassAmherst (University of Massachusetts Amherst)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I24603500","host_organization_name":"University of Massachusetts Amherst","host_organization_lineage":["https://openalex.org/I24603500"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computer Science Department Faculty Publication Series","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2126926732.pdf","grobid_xml":"https://content.openalex.org/works/W2126926732.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1590624824","https://openalex.org/W1973887944","https://openalex.org/W2044519929","https://openalex.org/W2062937620","https://openalex.org/W2109972881","https://openalex.org/W2120865735","https://openalex.org/W2160320069","https://openalex.org/W2171067698","https://openalex.org/W3022858172"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2156434174","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2081517010","https://openalex.org/W2121496884","https://openalex.org/W2387910809","https://openalex.org/W3200375535"],"abstract_inverted_index":{"Data":[0],"analysis":[1,36],"and":[2,9,107,111,138,175,185],"visualization":[3,62],"is":[4],"strongly":[5],"influenced":[6],"by":[7],"noise":[8,10,35,76,176],"filters.":[11],"There":[12],"are":[13,25],"multiple":[14],"sources":[15],"of":[16,37,52,74,80,92,127,153,169,194,208,216],"\"noise\"":[17],"in":[18,115],"microarray":[19],"data":[20,222],"analysis,":[21],"but":[22],"signal/noise":[23,202],"ratios":[24],"rarely":[26],"optimized,":[27],"or":[28,204],"even":[29],"considered.":[30],"Here,":[31],"we":[32],"report":[33],"a":[34,38,143,158,191],"novel":[39],"13":[40],"million":[41],"oligonucleotide":[42],"dataset":[43],"-":[44],"25":[45],"human":[46],"U133A":[47],"(/spl":[48],"sim/500,000":[49],"features)":[50],"profiles":[51],"patient":[53,90],"muscle":[54],"biopsies.":[55],"We":[56,95,149,189],"use":[57],"our":[58],"recently":[59],"described":[60],"interactive":[61,118,196],"tool,":[63],"the":[64,72,113,125,134,147,167,170,200,205,214,217],"hierarchical":[65],"clustering":[66,87,108,135],"explorer":[67],"(HCE)":[68],"to":[69,122,198,212],"systemically":[70],"address":[71],"effect":[73,160,215],"different":[75],"filters":[77],"on":[78,161,221],"resolution":[79],"arrays":[81],"into":[82,88],"\"correct\"":[83],"biological":[84,171,219],"groups":[85,91],"(unsupervised":[86],"three":[89,129,155,210],"known":[93],"diagnosis).":[94],"varied":[96],"probe":[97],"set":[98],"interpretation":[99],"methods":[100],"(MAS":[101],"5.0,":[102,180],"RMA),":[103],"\"present":[104],"call\"":[105],"filters,":[106],"linkage":[109],"methods,":[110],"investigated":[112],"results":[114,136],"HCE.":[116],"HCE's":[117],"features":[119],"enabled":[120],"us":[121],"quickly":[123],"see":[124],"impact":[126],"these":[128,154,209],"variables.":[130],"Dendrogram":[131],"displays":[132,141],"showed":[133],"systematically,":[137],"color":[139],"mosaic":[140],"provided":[142],"visual":[144],"support":[145],"for":[146],"results.":[148],"show":[150],"that":[151],"each":[152],"variables":[156,211],"has":[157],"strong":[159],"unsupervised":[162],"clustering.":[163],"For":[164],"this":[165],"dataset,":[166],"strength":[168],"variable":[172,220],"was":[173],"maximized,":[174],"minimized,":[177],"using":[178,195],"MAS":[179],"10%":[181],"present":[182],"call":[183],"filter,":[184],"average":[186],"group":[187],"linkage.":[188],"propose":[190],"general":[192],"method":[193],"tools":[197],"identify":[199],"optimal":[201,206],"balance":[203],"combination":[207],"maximize":[213],"desired":[218],"interpretation.":[223]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}