{"id":"https://openalex.org/W2132844342","doi":"https://doi.org/10.1093/bioinformatics/bti355","title":"Gene-Expression Omnibus integration and clustering Tools in SeqExpress","display_name":"Gene-Expression Omnibus integration and clustering Tools in SeqExpress","publication_year":2005,"publication_date":"2005-03-03","ids":{"openalex":"https://openalex.org/W2132844342","doi":"https://doi.org/10.1093/bioinformatics/bti355","mag":"2132844342","pmid":"https://pubmed.ncbi.nlm.nih.gov/15746290"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bti355","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti355","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/10/2550/48971846/bioinformatics_21_10_2550.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/21/10/2550/48971846/bioinformatics_21_10_2550.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056677361","display_name":"John Boyle","orcid":"https://orcid.org/0000-0002-5378-5361"},"institutions":[{"id":"https://openalex.org/I78559203","display_name":"FedEx (United States)","ror":"https://ror.org/04ps7x844","country_code":"US","type":"company","lineage":["https://openalex.org/I78559203"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"J. Boyle","raw_affiliation_strings":["john@seqexpress.com","Holbeck George Street, Cambridge CB4 1AJ, UK#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"john@seqexpress.com","institution_ids":["https://openalex.org/I78559203"]},{"raw_affiliation_string":"Holbeck George Street, Cambridge CB4 1AJ, UK#TAB#","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5056677361"],"corresponding_institution_ids":["https://openalex.org/I78559203"],"apc_list":null,"apc_paid":null,"fwci":0.6317,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.67275553,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"21","issue":"10","first_page":"2550","last_page":"2551"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9775999784469604,"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":0.9775999784469604,"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":0.006500000134110451,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.00139999995008111,"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/computer-science","display_name":"Computer science","score":0.7898293733596802},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6596423983573914},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6397982835769653},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5669640302658081},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5259031653404236},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.49274566769599915},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.44946035742759705},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.43119072914123535},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.4177856743335724},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.16784340143203735},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1658765971660614},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1263534128665924},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1158917248249054},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.11104074120521545},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09351128339767456}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7898293733596802},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6596423983573914},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6397982835769653},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5669640302658081},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5259031653404236},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.49274566769599915},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.44946035742759705},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.43119072914123535},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.4177856743335724},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.16784340143203735},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1658765971660614},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1263534128665924},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1158917248249054},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.11104074120521545},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09351128339767456},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"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":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020407","descriptor_name":"Internet","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},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025341","descriptor_name":"Principal Component Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bti355","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti355","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/10/2550/48971846/bioinformatics_21_10_2550.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:15746290","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/15746290","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/bti355","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bti355","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/21/10/2550/48971846/bioinformatics_21_10_2550.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":false,"pdf":false},"content_urls":null,"referenced_works_count":5,"referenced_works":["https://openalex.org/W2020541351","https://openalex.org/W2081331317","https://openalex.org/W2103017472","https://openalex.org/W2118770381","https://openalex.org/W2127391575"],"related_works":["https://openalex.org/W4231704780","https://openalex.org/W2083794993","https://openalex.org/W352609212","https://openalex.org/W1511772879","https://openalex.org/W4379115841","https://openalex.org/W4200340037","https://openalex.org/W608917066","https://openalex.org/W4283652261","https://openalex.org/W585424826","https://openalex.org/W564602992"],"abstract_inverted_index":{"UNLABELLED:":[0],"SeqExpress,":[1],"a":[2,11,54,83,109,153],"gene-expression":[3],"analysis":[4,47],"suite,":[5],"has":[6,111],"been":[7,25,112],"extended":[8],"to":[9,27,63,81,96,127,191],"offer":[10],"number":[12,130],"of":[13,31,44,74,85,102,131],"cluster":[14,21,46,62,104],"generation,":[15],"refinement":[16],"and":[17,34,98,143,159,168,188],"visualization":[18],"techniques.":[19],"The":[20,42,122],"generation":[22,105],"methods":[23],"have":[24],"specialized":[26],"deal":[28],"with":[29,117,179],"aspects":[30],"the":[32,90,100,103,118,128,135,172],"sparseness":[33],"extreme":[35],"values":[36],"that":[37,138],"occur":[38],"within":[39,89],"microarray":[40],"data.":[41],"results":[43,101,133],"such":[45],"can":[48,140],"then":[49],"be":[50,141],"refined":[51],"using":[52,79,146],"either:":[53],"functional":[55],"enrichment":[56],"based":[57,87],"procedure,":[58],"which":[59,114],"examines":[60],"each":[61],"see":[64],"if":[65],"it":[66],"possesses":[67],"an":[68],"unusually":[69],"high":[70],"or":[71,77,185],"low":[72],"concentration":[73],"ontology":[75],"terms;":[76],"by":[78,193],"Expectation-Maximization":[80],"find":[82],"mixture":[84],"model":[86],"distributions":[88],"datasets.":[91],"Visualizations":[92],"are":[93],"provided":[94],"both":[95],"explore":[97],"compare":[99],"algorithms.":[106],"In":[107],"addition,":[108],"tool":[110,123],"developed":[113],"integrates":[115],"SeqExpress":[116,149,175],"Gene-Expression":[119],"Omnibus":[120],"repository.":[121],"provides":[124],"seamless":[125],"access":[126],"large":[129],"experimental":[132],"in":[134],"repository,":[136],"so":[137],"they":[139],"visualized":[142],"analysed":[144],"locally":[145],"SeqExpress.":[147],"AVAILABILITY:":[148],"is":[150,166,169,176,189],"available":[151,167],"as":[152],"6":[154],"MB":[155],"download":[156],"from":[157],"http://www.seqexpress.com":[158],"runs":[160],"under":[161],"Windows.":[162],"A":[163],"server-based":[164],"version":[165],"required":[170],"for":[171],"GEO":[173],"integration.":[174],"not":[177],"affiliated":[178],"any":[180],"academic":[181],"institution,":[182],"funding":[183],"body":[184],"commercial":[186],"organization":[187],"free":[190],"use":[192],"all.":[194]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-19T21:40:30.786675","created_date":"2025-10-10T00:00:00"}
