{"id":"https://openalex.org/W2168525657","doi":"https://doi.org/10.1093/nar/gkf414","title":"Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods","display_name":"Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods","publication_year":2002,"publication_date":"2002-07-01","ids":{"openalex":"https://openalex.org/W2168525657","doi":"https://doi.org/10.1093/nar/gkf414","mag":"2168525657","pmid":"https://pubmed.ncbi.nlm.nih.gov/12087178"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkf414","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/gkf414","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":null,"any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013706483","display_name":"Kerby Shedden","orcid":"https://orcid.org/0000-0001-7222-6664"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan\u2013Ann Arbor","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"K. Shedden","raw_affiliation_strings":["Department of Statistics, University of Michigan, Ann Arbor, MI 48109-1285, USA. kshedden@umich.edu","Department of Statistics, University of Michigan, Ann Arbor, MI 48109-1285, USA"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of Michigan, Ann Arbor, MI 48109-1285, USA. kshedden@umich.edu","institution_ids":["https://openalex.org/I27837315"]},{"raw_affiliation_string":"Department of Statistics, University of Michigan, Ann Arbor, MI 48109-1285, USA","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5013706483"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":2.521,"has_fulltext":false,"cited_by_count":83,"citation_normalized_percentile":{"value":0.89886762,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"30","issue":"13","first_page":"2920","last_page":"2929"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9973999857902527,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.9961000084877014,"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/biology","display_name":"Biology","score":0.8298695087432861},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.6498210430145264},{"id":"https://openalex.org/keywords/synchronization","display_name":"Synchronization (alternating current)","score":0.5772051811218262},{"id":"https://openalex.org/keywords/cell-cycle","display_name":"Cell cycle","score":0.5721595287322998},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5550671219825745},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5283100008964539},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5259804129600525},{"id":"https://openalex.org/keywords/cyclin-dependent-kinase-1","display_name":"Cyclin-dependent kinase 1","score":0.4981389045715332},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46243512630462646},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.44582781195640564},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.35177868604660034},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09512874484062195},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.08087417483329773}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8298695087432861},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.6498210430145264},{"id":"https://openalex.org/C2778562939","wikidata":"https://www.wikidata.org/wiki/Q1298791","display_name":"Synchronization (alternating current)","level":3,"score":0.5772051811218262},{"id":"https://openalex.org/C29537977","wikidata":"https://www.wikidata.org/wiki/Q188941","display_name":"Cell cycle","level":3,"score":0.5721595287322998},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5550671219825745},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5283100008964539},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5259804129600525},{"id":"https://openalex.org/C120504264","wikidata":"https://www.wikidata.org/wiki/Q1147372","display_name":"Cyclin-dependent kinase 1","level":4,"score":0.4981389045715332},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46243512630462646},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.44582781195640564},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.35177868604660034},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09512874484062195},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.08087417483329773},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002455","descriptor_name":"Cell Division","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002455","descriptor_name":"Cell Division","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002455","descriptor_name":"Cell Division","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005800","descriptor_name":"Genes, Fungal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015966","descriptor_name":"Gene Expression Regulation, Fungal","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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/nar/gkf414","is_oa":false,"landing_page_url":"https://doi.org/10.1093/nar/gkf414","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":false,"is_in_doaj":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12087178","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12087178","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:155335","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC117069","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},{"id":"pmh:oai:europepmc.org:155335","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/117069","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:117069","is_oa":true,"landing_page_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:117069","is_oa":true,"landing_page_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309652","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W136346993","https://openalex.org/W1483505747","https://openalex.org/W1503636374","https://openalex.org/W1535507971","https://openalex.org/W1849539769","https://openalex.org/W1978487487","https://openalex.org/W1989966898","https://openalex.org/W1990000671","https://openalex.org/W1994079778","https://openalex.org/W1996697473","https://openalex.org/W2014044453","https://openalex.org/W2016125228","https://openalex.org/W2052072891","https://openalex.org/W2054774141","https://openalex.org/W2070708981","https://openalex.org/W2103453943","https://openalex.org/W2113387206","https://openalex.org/W2113654344","https://openalex.org/W2127136746","https://openalex.org/W2132585078","https://openalex.org/W2133504259","https://openalex.org/W2135000328","https://openalex.org/W2142460132","https://openalex.org/W2143631823","https://openalex.org/W2146264532","https://openalex.org/W2148541040","https://openalex.org/W2148602507","https://openalex.org/W2150926065","https://openalex.org/W2159309601","https://openalex.org/W2168157737"],"related_works":["https://openalex.org/W4315558101","https://openalex.org/W3200271510","https://openalex.org/W63366483","https://openalex.org/W1516770101","https://openalex.org/W1897466773","https://openalex.org/W2357011584","https://openalex.org/W3123797028","https://openalex.org/W2889677605","https://openalex.org/W2347624711","https://openalex.org/W2366424044"],"abstract_inverted_index":{"Microarray":[0],"analysis":[1],"of":[2,19,33,45,79,91,99,106,119,143,173,184,187],"gene":[3,150,188],"expression":[4,57,189],"during":[5,190],"the":[6,13,49,53,56,60,73,77,96,107,122,131,170,174,180,185,191,200,204],"yeast":[7],"division":[8],"cycle":[9],"has":[10],"led":[11],"to":[12,212],"proposal":[14],"that":[15,104],"a":[16,27,88,127,140,149,209],"significant":[17],"number":[18],"genes":[20,82,137],"in":[21,26,55,59,72,83,154,162,203,218],"Saccharomyces":[22],"cerevisiae":[23],"are":[24,86,208],"expressed":[25],"cell-cycle-specific":[28],"manner.":[29],"Four":[30],"different":[31,84,128,147],"methods":[32],"synchronization":[34,134,176],"were":[35],"used":[36],"for":[37,81],"cell-cycle":[38],"analysis.":[39],"Randomized":[40],"data":[41],"exhibit":[42],"periodic":[43],"patterns":[44,118],"lesser":[46],"strength":[47],"than":[48],"experimental":[50],"data.":[51,74],"Thus":[52],"cyclicities":[54,202],"measurements":[58],"four":[61,175],"experiments":[62,85,108,207],"presented":[63],"do":[64],"not":[65,216],"arise":[66],"from":[67,130],"chance":[68],"fluctuations":[69],"or":[70],"noise":[71],"However,":[75],"when":[76],"degree":[78,90],"cyclicity":[80,153,161],"compared,":[87],"large":[89],"non-reproducibility":[92],"is":[93],"found.":[94],"Re-examining":[95],"phase":[97],"timing":[98],"peak":[100],"expression,":[101],"we":[102],"find":[103],"three":[105,206],"(those":[109],"using":[110],"alpha-factor,":[111],"CDC28":[112],"and":[113,214],"CDC15":[114],"synchronization)":[115],"show":[116,139,158],"consistent":[117],"phasing,":[120],"but":[121],"elutriation":[123,166],"synchrony":[124],"results":[125],"demonstrate":[126],"pattern":[129],"other":[132,205],"arrest-release":[133],"methods.":[135],"Specific":[136],"can":[138,157],"wide":[141],"range":[142],"cyclical":[144],"behavior":[145],"between":[146],"experiments;":[148],"with":[151],"high":[152],"one":[155],"experiment":[156],"essentially":[159],"no":[160],"another":[163],"experiment.":[164],"The":[165],"experiment,":[167],"possibly":[168],"being":[169],"least":[171],"perturbing":[172],"methods,":[177],"may":[178,215],"give":[179],"most":[181],"accurate":[182],"characterization":[183],"state":[186],"normal,":[192],"unperturbed":[193,219],"cell":[194],"cycle.":[195],"Under":[196],"this":[197],"alternative":[198],"explanation,":[199],"observed":[201],"stress":[210],"response":[211],"synchronization,":[213],"reproduce":[217],"cells.":[220]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
