{"id":"https://openalex.org/W4382198867","doi":"https://doi.org/10.1093/bib/bbad241","title":"<i>E</i>-value: a superior alternative to <i>P</i>-value and its adjustments in DNA methylation studies","display_name":"<i>E</i>-value: a superior alternative to <i>P</i>-value and its adjustments in DNA methylation studies","publication_year":2023,"publication_date":"2023-06-14","ids":{"openalex":"https://openalex.org/W4382198867","doi":"https://doi.org/10.1093/bib/bbad241","pmid":"https://pubmed.ncbi.nlm.nih.gov/37369639"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad241","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1093/bib/bbad241","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10359086/pdf/bbad241.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032964730","display_name":"Yifan Yang","orcid":"https://orcid.org/0000-0001-9127-168X"},"institutions":[{"id":"https://openalex.org/I21945476","display_name":"Shanghai Normal University","ror":"https://ror.org/01cxqmw89","country_code":"CN","type":"education","lineage":["https://openalex.org/I21945476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yifan Yang","raw_affiliation_strings":["Department of Mathematics, Shanghai Normal University , Shanghai , China","Transwarp Technology Co., LTD , Shanghai , China"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Shanghai Normal University , Shanghai , China","institution_ids":["https://openalex.org/I21945476"]},{"raw_affiliation_string":"Transwarp Technology Co., LTD , Shanghai , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115588590","display_name":"Haoyuan Liu","orcid":"https://orcid.org/0000-0002-6702-7406"},"institutions":[{"id":"https://openalex.org/I21945476","display_name":"Shanghai Normal University","ror":"https://ror.org/01cxqmw89","country_code":"CN","type":"education","lineage":["https://openalex.org/I21945476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoyuan Liu","raw_affiliation_strings":["Department of Mathematics, Shanghai Normal University , Shanghai , China"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Shanghai Normal University , Shanghai , China","institution_ids":["https://openalex.org/I21945476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083956868","display_name":"Yi Liu","orcid":"https://orcid.org/0000-0002-8801-9317"},"institutions":[{"id":"https://openalex.org/I2802390878","display_name":"Sir Run Run Shaw Hospital","ror":"https://ror.org/00ka6rp58","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802390878"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Liu","raw_affiliation_strings":["Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","Zhejiang University , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","institution_ids":["https://openalex.org/I2802390878"]},{"raw_affiliation_string":"Zhejiang University , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","institution_ids":["https://openalex.org/I2802390878","https://openalex.org/I76130692"]},{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I2802390878","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101622398","display_name":"Liyuan Zhou","orcid":"https://orcid.org/0000-0001-7485-8163"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]},{"id":"https://openalex.org/I2802390878","display_name":"Sir Run Run Shaw Hospital","ror":"https://ror.org/00ka6rp58","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802390878"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liyuan Zhou","raw_affiliation_strings":["Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","Zhejiang University , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","institution_ids":["https://openalex.org/I2802390878"]},{"raw_affiliation_string":"Zhejiang University , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","institution_ids":["https://openalex.org/I2802390878","https://openalex.org/I76130692"]},{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I2802390878","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021047181","display_name":"Xiaoqi Zheng","orcid":"https://orcid.org/0000-0002-1832-4404"},"institutions":[{"id":"https://openalex.org/I21945476","display_name":"Shanghai Normal University","ror":"https://ror.org/01cxqmw89","country_code":"CN","type":"education","lineage":["https://openalex.org/I21945476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoqi Zheng","raw_affiliation_strings":["Department of Mathematics, Shanghai Normal University , Shanghai , China"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Shanghai Normal University , Shanghai , China","institution_ids":["https://openalex.org/I21945476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004998206","display_name":"Rong\u2010Xian Yue","orcid":"https://orcid.org/0000-0001-6899-4636"},"institutions":[{"id":"https://openalex.org/I21945476","display_name":"Shanghai Normal University","ror":"https://ror.org/01cxqmw89","country_code":"CN","type":"education","lineage":["https://openalex.org/I21945476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rongxian Yue","raw_affiliation_strings":["Department of Mathematics, Shanghai Normal University , Shanghai , China"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Shanghai Normal University , Shanghai , China","institution_ids":["https://openalex.org/I21945476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051412894","display_name":"David L. Mattson","orcid":"https://orcid.org/0000-0002-5401-0269"},"institutions":[{"id":"https://openalex.org/I25041050","display_name":"Augusta University","ror":"https://ror.org/012mef835","country_code":"US","type":"education","lineage":["https://openalex.org/I25041050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David L Mattson","raw_affiliation_strings":["Augusta University , Medical College of Georgia, , Augusta, GA , USA","Department of Physiology , Medical College of Georgia, , Augusta, GA , USA","Department of Physiology, Medical College of Georgia, Augusta University, Augusta, GA, USA"],"affiliations":[{"raw_affiliation_string":"Augusta University , Medical College of Georgia, , Augusta, GA , USA","institution_ids":["https://openalex.org/I25041050"]},{"raw_affiliation_string":"Department of Physiology , Medical College of Georgia, , Augusta, GA , USA","institution_ids":["https://openalex.org/I25041050"]},{"raw_affiliation_string":"Department of Physiology, Medical College of Georgia, Augusta University, Augusta, GA, USA","institution_ids":["https://openalex.org/I25041050"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057324868","display_name":"Srividya Kidambi","orcid":"https://orcid.org/0000-0003-1589-5268"},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Srividya Kidambi","raw_affiliation_strings":["Department of Medicine, Medical College of Wisconsin , Milwaukee, WI , USA"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, Medical College of Wisconsin , Milwaukee, WI , USA","institution_ids":["https://openalex.org/I204308271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081888342","display_name":"Mingyu Liang","orcid":"https://orcid.org/0000-0002-6970-989X"},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mingyu Liang","raw_affiliation_strings":["Center of Systems Molecular Medicine , Department of Physiology, , Milwaukee, WI , USA","Medical College of Wisconsin , Department of Physiology, , Milwaukee, WI , USA","Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA"],"affiliations":[{"raw_affiliation_string":"Center of Systems Molecular Medicine , Department of Physiology, , Milwaukee, WI , USA","institution_ids":[]},{"raw_affiliation_string":"Medical College of Wisconsin , Department of Physiology, , Milwaukee, WI , USA","institution_ids":["https://openalex.org/I204308271"]},{"raw_affiliation_string":"Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA","institution_ids":["https://openalex.org/I204308271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100714943","display_name":"Pengyuan Liu","orcid":"https://orcid.org/0000-0002-8386-8416"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]},{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]},{"id":"https://openalex.org/I2802390878","display_name":"Sir Run Run Shaw Hospital","ror":"https://ror.org/00ka6rp58","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802390878"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Pengyuan Liu","raw_affiliation_strings":["Center of Systems Molecular Medicine , Department of Physiology, , Milwaukee, WI , USA","Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","Medical College of Wisconsin , Department of Physiology, , Milwaukee, WI , USA","Zhejiang University , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, Hangzhou, China"],"affiliations":[{"raw_affiliation_string":"Center of Systems Molecular Medicine , Department of Physiology, , Milwaukee, WI , USA","institution_ids":[]},{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","institution_ids":["https://openalex.org/I2802390878"]},{"raw_affiliation_string":"Medical College of Wisconsin , Department of Physiology, , Milwaukee, WI , USA","institution_ids":["https://openalex.org/I204308271"]},{"raw_affiliation_string":"Zhejiang University , Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, , Hangzhou , China","institution_ids":["https://openalex.org/I2802390878","https://openalex.org/I76130692"]},{"raw_affiliation_string":"Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I2802390878","https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101848102","display_name":"Xiaoqing Pan","orcid":"https://orcid.org/0000-0002-3559-5337"},"institutions":[{"id":"https://openalex.org/I21945476","display_name":"Shanghai Normal University","ror":"https://ror.org/01cxqmw89","country_code":"CN","type":"education","lineage":["https://openalex.org/I21945476"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaoqing Pan","raw_affiliation_strings":["Department of Mathematics, Shanghai Normal University , Shanghai , China"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Shanghai Normal University , Shanghai , China","institution_ids":["https://openalex.org/I21945476"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5100714943","https://openalex.org/A5101848102"],"corresponding_institution_ids":["https://openalex.org/I204308271","https://openalex.org/I21945476","https://openalex.org/I2802390878","https://openalex.org/I76130692"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.1556,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.58310208,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"24","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","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/T10269","display_name":"Epigenetics and DNA Methylation","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/T11928","display_name":"Genetic Syndromes and Imprinting","score":0.9707000255584717,"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/T11482","display_name":"RNA modifications and cancer","score":0.9527000188827515,"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/benchmarking","display_name":"Benchmarking","score":0.715093195438385},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.6012922525405884},{"id":"https://openalex.org/keywords/statistical-power","display_name":"Statistical power","score":0.5998697280883789},{"id":"https://openalex.org/keywords/decitabine","display_name":"Decitabine","score":0.5287477374076843},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.4689680337905884},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.4571828842163086},{"id":"https://openalex.org/keywords/value","display_name":"Value (mathematics)","score":0.4481401741504669},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44175225496292114},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42203351855278015},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3979473412036896},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34115561842918396},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3157627582550049},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26677119731903076},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2145959436893463},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1336129605770111}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.715093195438385},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.6012922525405884},{"id":"https://openalex.org/C96608239","wikidata":"https://www.wikidata.org/wiki/Q1199823","display_name":"Statistical power","level":2,"score":0.5998697280883789},{"id":"https://openalex.org/C2780235182","wikidata":"https://www.wikidata.org/wiki/Q1181878","display_name":"Decitabine","level":5,"score":0.5287477374076843},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4689680337905884},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4571828842163086},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.4481401741504669},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44175225496292114},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42203351855278015},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3979473412036896},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34115561842918396},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3157627582550049},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26677119731903076},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2145959436893463},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1336129605770111},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012372","descriptor_name":"ROC Curve","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018899","descriptor_name":"CpG Islands","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},{"descriptor_ui":"D019175","descriptor_name":"DNA Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051381","descriptor_name":"Rats","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad241","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1093/bib/bbad241","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37369639","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37369639","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10359086","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10359086","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10359086/pdf/bbad241.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:10359086","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10359086","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10359086/pdf/bbad241.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2582230382","display_name":null,"funder_award_id":"20JC1413800","funder_id":"https://openalex.org/F4320309612","funder_display_name":"Natural Science Foundation of Shanghai"},{"id":"https://openalex.org/G4736470801","display_name":null,"funder_award_id":"HL149620","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5460385124","display_name":null,"funder_award_id":"15SFRN23910002","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"},{"id":"https://openalex.org/G6623863905","display_name":null,"funder_award_id":"82072857","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320306230","display_name":"American Heart Association","ror":"https://ror.org/013kjyp64"},{"id":"https://openalex.org/F4320309612","display_name":"Natural Science Foundation of Shanghai","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322374","display_name":"Shanghai Normal University","ror":"https://ror.org/01cxqmw89"},{"id":"https://openalex.org/F4320322676","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68"},{"id":"https://openalex.org/F4320322927","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4382198867.pdf","grobid_xml":"https://content.openalex.org/works/W4382198867.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1509280974","https://openalex.org/W1984114719","https://openalex.org/W2000225203","https://openalex.org/W2018742491","https://openalex.org/W2025651303","https://openalex.org/W2037592609","https://openalex.org/W2059099579","https://openalex.org/W2075418882","https://openalex.org/W2081814119","https://openalex.org/W2098332282","https://openalex.org/W2106340111","https://openalex.org/W2110065044","https://openalex.org/W2113818262","https://openalex.org/W2115012618","https://openalex.org/W2116514399","https://openalex.org/W2126414144","https://openalex.org/W2131176327","https://openalex.org/W2131374955","https://openalex.org/W2150194502","https://openalex.org/W2150215887","https://openalex.org/W2154814024","https://openalex.org/W2156124720","https://openalex.org/W2158774461","https://openalex.org/W2186978757","https://openalex.org/W2281247410","https://openalex.org/W2293040502","https://openalex.org/W2408017125","https://openalex.org/W2476507049","https://openalex.org/W2544360569","https://openalex.org/W2550185754","https://openalex.org/W2790957875","https://openalex.org/W2803457956","https://openalex.org/W2891742382","https://openalex.org/W2909484358","https://openalex.org/W2922853138","https://openalex.org/W2924950986","https://openalex.org/W2951144892","https://openalex.org/W2971824678","https://openalex.org/W2980328779","https://openalex.org/W2983485493","https://openalex.org/W2996159484","https://openalex.org/W3044989759","https://openalex.org/W3122067158","https://openalex.org/W3139222214","https://openalex.org/W3144154879","https://openalex.org/W3170680323","https://openalex.org/W3187717145","https://openalex.org/W4205305706","https://openalex.org/W4220728292","https://openalex.org/W4225485759","https://openalex.org/W4229335502","https://openalex.org/W4229443644","https://openalex.org/W6676591658","https://openalex.org/W6769546971"],"related_works":["https://openalex.org/W2902329290","https://openalex.org/W2052355316","https://openalex.org/W2128056428","https://openalex.org/W2046964473","https://openalex.org/W2107880877","https://openalex.org/W2151182744","https://openalex.org/W2024490794","https://openalex.org/W2221018455","https://openalex.org/W1998349112","https://openalex.org/W2054863651"],"abstract_inverted_index":{"DNA":[0,249],"methylation":[1,23,250],"plays":[2],"a":[3,15,114,146,227],"crucial":[4],"role":[5],"in":[6,53,135,177],"transcriptional":[7],"regulation.":[8],"Reduced":[9],"representation":[10],"bisulfite":[11],"sequencing":[12],"(RRBS)":[13],"is":[14],"technique":[16],"of":[17,45,56,86,105,162,202,223,235],"increasing":[18,94],"use":[19,39,234],"for":[20,42,64,132],"analyzing":[21],"genome-wide":[22],"profiles.":[24],"Many":[25],"computational":[26],"tools":[27],"such":[28],"as":[29,63,119,145],"Metilene,":[30],"MethylKit,":[31],"BiSeq":[32],"and":[33,70,101,198,213,226,242,251],"DMRfinder":[34],"have":[35],"been":[36],"developed":[37],"to":[38,81,97,116,149],"RRBS":[40,136,167,221],"data":[41,222],"the":[43,46,75,83,124,128,141,160,233,245],"detection":[44,61,134,156],"differentially":[47],"methylated":[48],"regions":[49],"(DMRs)":[50],"potentially":[51],"involved":[52],"epigenetic":[54],"regulations":[55],"gene":[57,252],"expression.":[58,253],"For":[59],"DMR":[60,133,155],"tools,":[62],"countless":[65],"other":[66],"medical":[67],"applications,":[68],"P-values":[69,90,203],"their":[71,98],"adjustments":[72],"are":[73,91],"among":[74],"most":[76],"standard":[77],"reporting":[78],"statistics":[79],"used":[80],"assess":[82],"statistical":[84],"significance":[85],"biological":[87],"findings.":[88],"However,":[89],"coming":[92],"under":[93,195],"criticism":[95],"relating":[96],"questionable":[99],"accuracy":[100],"relatively":[102],"high":[103],"levels":[104],"false":[106,210],"positive":[107],"or":[108,204],"negative":[109,246],"indications.":[110],"Here,":[111],"we":[112,164],"propose":[113],"method":[115],"calculate":[117],"E-values,":[118,163],"likelihood":[120],"ratios":[121],"falling":[122],"into":[123,153],"null":[125],"hypothesis":[126],"over":[127,200],"entire":[129],"parameter":[130],"space,":[131],"data.":[137],"We":[138],"also":[139,208,243],"provide":[140],"R":[142],"package":[143],"'metevalue'":[144],"user-friendly":[147],"interface":[148],"implement":[150],"E-value":[151],"calculations":[152],"various":[154,166],"tools.":[157],"To":[158],"evaluate":[159],"performance":[161],"generated":[165],"benchmarking":[168,183],"datasets":[169],"using":[170,187,219],"our":[171],"simulator":[172],"'RRBSsim'":[173],"with":[174],"eight":[175],"samples":[176],"each":[178],"experimental":[179],"group.":[180],"Our":[181],"comprehensive":[182],"analyses":[184],"showed":[185],"that":[186,201],"E-values":[188,236],"not":[189],"only":[190],"significantly":[191],"improved":[192,244],"accuracy,":[193],"area":[194],"ROC":[196],"curve":[197],"power,":[199],"adjusted":[205],"P-values,":[206],"but":[207],"reduced":[209],"discovery":[211],"rates":[212],"type":[214],"I":[215],"errors.":[216],"In":[217],"applications":[218],"real":[220],"CRL":[224],"rats":[225],"clinical":[228],"trial":[229],"on":[230],"low-salt":[231],"diet,":[232],"detected":[237],"biologically":[238],"more":[239],"relevant":[240],"DMRs":[241],"association":[247],"between":[248]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2023-06-28T00:00:00"}
