{"id":"https://openalex.org/W2889180480","doi":"https://doi.org/10.1093/bioinformatics/bty778","title":"Differential methylation values in differential methylation analysis","display_name":"Differential methylation values in differential methylation analysis","publication_year":2018,"publication_date":"2018-09-01","ids":{"openalex":"https://openalex.org/W2889180480","doi":"https://doi.org/10.1093/bioinformatics/bty778","mag":"2889180480","pmid":"https://pubmed.ncbi.nlm.nih.gov/30184051"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty778","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty778","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1094/48967479/bioinformatics_35_7_1094.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1094/48967479/bioinformatics_35_7_1094.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101647373","display_name":"Changchun Xie","orcid":"https://orcid.org/0000-0002-1843-4099"},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Changchun Xie","raw_affiliation_strings":["Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082503230","display_name":"Yuet\u2010Kin Leung","orcid":"https://orcid.org/0000-0003-2063-277X"},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuet-Kin Leung","raw_affiliation_strings":["Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100626535","display_name":"Aimin Chen","orcid":"https://orcid.org/0000-0001-9713-6438"},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aimin Chen","raw_affiliation_strings":["Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA","institution_ids":["https://openalex.org/I63135867"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110095231","display_name":"Dingxin Long","orcid":null},"institutions":[{"id":"https://openalex.org/I91935597","display_name":"University of South China","ror":"https://ror.org/03mqfn238","country_code":"CN","type":"education","lineage":["https://openalex.org/I91935597"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ding-Xin Long","raw_affiliation_strings":["School of Public Health, University of South China, Hengyang, Hunan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Public Health, University of South China, Hengyang, Hunan, China","institution_ids":["https://openalex.org/I91935597"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010619424","display_name":"Catherine Hoyo","orcid":null},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Catherine Hoyo","raw_affiliation_strings":["Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA","institution_ids":["https://openalex.org/I137902535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028510658","display_name":"Shuk\u2010Mei Ho","orcid":"https://orcid.org/0000-0001-9369-7342"},"institutions":[{"id":"https://openalex.org/I63135867","display_name":"University of Cincinnati","ror":"https://ror.org/01e3m7079","country_code":"US","type":"education","lineage":["https://openalex.org/I63135867"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuk-Mei Ho","raw_affiliation_strings":["Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA","institution_ids":["https://openalex.org/I63135867"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101647373"],"corresponding_institution_ids":["https://openalex.org/I63135867"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8946,"has_fulltext":true,"cited_by_count":71,"citation_normalized_percentile":{"value":0.86502608,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"35","issue":"7","first_page":"1094","last_page":"1097"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.8269000053405762,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.8269000053405762,"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":0.033399999141693115,"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/T11928","display_name":"Genetic Syndromes and Imprinting","score":0.011900000274181366,"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/linear-regression","display_name":"Linear regression","score":0.7739136219024658},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.6717713475227356},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.6444471478462219},{"id":"https://openalex.org/keywords/regression-analysis","display_name":"Regression analysis","score":0.6383867263793945},{"id":"https://openalex.org/keywords/differential","display_name":"Differential (mechanical device)","score":0.600622832775116},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.5359315276145935},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.49272945523262024},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4863193929195404},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16840997338294983},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1166539192199707},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.06470644474029541},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.05888822674751282}],"concepts":[{"id":"https://openalex.org/C48921125","wikidata":"https://www.wikidata.org/wiki/Q10861030","display_name":"Linear regression","level":2,"score":0.7739136219024658},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.6717713475227356},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.6444471478462219},{"id":"https://openalex.org/C152877465","wikidata":"https://www.wikidata.org/wiki/Q208042","display_name":"Regression analysis","level":2,"score":0.6383867263793945},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.600622832775116},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.5359315276145935},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.49272945523262024},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4863193929195404},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16840997338294983},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1166539192199707},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.06470644474029541},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.05888822674751282},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty778","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty778","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1094/48967479/bioinformatics_35_7_1094.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30184051","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30184051","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},{"id":"pmh:oai:europepmc.org:6057926","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6449748","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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty778","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty778","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/7/1094/48967479/bioinformatics_35_7_1094.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2702429622","display_name":null,"funder_award_id":"RC4 ES019755","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G3831105557","display_name":null,"funder_award_id":"P30-ES006096","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3954792654","display_name":null,"funder_award_id":"ES006096","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5492848456","display_name":null,"funder_award_id":"ES006096","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G6797967596","display_name":null,"funder_award_id":"R01 ES020349","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G7280013184","display_name":null,"funder_award_id":"P30-ES006096","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G793507617","display_name":null,"funder_award_id":"P30 ES006096","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G8997535963","display_name":null,"funder_award_id":"R01 ES028277","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2889180480.pdf","grobid_xml":"https://content.openalex.org/works/W2889180480.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1903636186","https://openalex.org/W2056040742","https://openalex.org/W2074746593","https://openalex.org/W2081754986","https://openalex.org/W2092075890","https://openalex.org/W2206368938","https://openalex.org/W2329888282","https://openalex.org/W2347155688","https://openalex.org/W2515727304","https://openalex.org/W2792118266"],"related_works":["https://openalex.org/W1976866108","https://openalex.org/W2610868774","https://openalex.org/W2092994918","https://openalex.org/W2390006526","https://openalex.org/W3216594821","https://openalex.org/W1915333409","https://openalex.org/W3215700490","https://openalex.org/W2393341384","https://openalex.org/W4289356671","https://openalex.org/W4363647291"],"abstract_inverted_index":{"MOTIVATION:":[0],"Both":[1],"\u03b2-value":[2,29,156,211],"and":[3,35,125,148],"M-value":[4,15,41,69,75,121,144,167],"have":[5,112],"been":[6],"used":[7,44],"as":[8],"metrics":[9],"to":[10,37,55,58,90,116,137],"measure":[11],"methylation":[12,25,48,64,74,94,140],"levels.":[13,26],"The":[14,206,238],"is":[16,30,43,51,87,171,176,242],"more":[17,32],"statistically":[18,119],"valid":[19],"for":[20,45,240,248],"the":[21,28,60,66,82,92,103,109,118,126,151,164,173,177,180,190,200,245],"differential":[22,47,63,73,93,139],"analysis":[23],"of":[24,62],"However,":[27],"much":[31],"biologically":[33,127],"interpretable":[34,128],"needs":[36],"be":[38,78,100,204],"reported":[39],"when":[40,221],"method":[42,174,184,202],"conducting":[46],"analysis.":[49],"There":[50],"an":[52],"urgent":[53],"need":[54],"know":[56],"how":[57],"interpret":[59],"degree":[61],"from":[65,81,102,143,155,210],"M-value.":[67],"In":[68,130],"linear":[70,122,145,157,168,212],"regression":[71,123,146,158,169,213],"model,":[72],"\u0394M":[76],"can":[77,215],"easily":[79],"obtained":[80,101,154,209],"coefficient":[83,104],"estimate,":[84],"but":[85],"it":[86,98],"not":[88,195,224,231],"straightforward":[89],"get":[91],"\u03b2-value,":[95],"\u0394\u03b2":[96,142,152,207],"since":[97],"cannot":[99],"alone.":[105],"RESULTS:":[106],"To":[107],"fill":[108],"gap,":[110],"we":[111],"built":[113],"a":[114],"bridge":[115],"connect":[117],"sound":[120],"model":[124,147,170,214],"\u0394\u03b2.":[129],"this":[131],"article,":[132],"three":[133],"methods":[134],"were":[135],"proposed":[136],"calculate":[138],"values,":[141],"compared":[149],"with":[150],"directly":[153,208],"model.":[159],"We":[160],"showed":[161],"that":[162,166],"under":[163],"condition":[165],"correct,":[172],"M-model-coef":[175],"best":[178],"among":[179],"four":[181],"methods.":[182],"M-model-M-mean":[183,201],"works":[185],"very":[186,217],"well":[187],"too.":[188],"If":[189],"coefficients":[191],"\u03b10,":[192],"\u03b12,\u2026\u03b1p":[193],"are":[194,223,230,260],"given":[196],"(as":[197],"'MethLAB'":[198],"package),":[199],"should":[203],"used.":[205],"give":[216],"biased":[218],"results,":[219],"especially":[220],"M-values":[222],"in":[225,232],"(-2,":[226],"2)":[227],"or":[228],"\u03b2-values":[229],"(0.2,":[233],"0.8).":[234],"AVAILABILITY":[235],"AND":[236],"IMPLEMENTATION:":[237],"dataset":[239],"example":[241],"available":[243,261],"at":[244,262],"National":[246],"Center":[247],"Biotechnology":[249],"Information":[250],"Gene":[251],"Expression":[252],"Omnibus":[253],"repository,":[254],"GSE104778.":[255],"SUPPLEMENTARY":[256],"INFORMATION:":[257],"Supplementary":[258],"data":[259],"Bioinformatics":[263],"online.":[264]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":16},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":4}],"updated_date":"2026-07-14T08:27:34.040176","created_date":"2025-10-10T00:00:00"}
