{"id":"https://openalex.org/W2487261336","doi":"https://doi.org/10.1093/bib/bbw063","title":"Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns","display_name":"Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns","publication_year":2016,"publication_date":"2016-07-19","ids":{"openalex":"https://openalex.org/W2487261336","doi":"https://doi.org/10.1093/bib/bbw063","mag":"2487261336","pmid":"https://pubmed.ncbi.nlm.nih.gov/27436122"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbw063","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbw063","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070230762","display_name":"Xiaofei Yang","orcid":"https://orcid.org/0000-0002-5118-7755"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaofei Yang","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083753621","display_name":"Lin Gao","orcid":"https://orcid.org/0000-0002-1781-4671"},"institutions":[{"id":"https://openalex.org/I149594827","display_name":"Xidian University","ror":"https://ror.org/05s92vm98","country_code":"CN","type":"education","lineage":["https://openalex.org/I149594827"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Gao","raw_affiliation_strings":["School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi, China","institution_ids":["https://openalex.org/I149594827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076619069","display_name":"Shihua Zhang","orcid":"https://orcid.org/0000-0003-0192-7118"},"institutions":[{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shihua Zhang","raw_affiliation_strings":["National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210095018","https://openalex.org/I4210120485","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5076619069"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":6.169,"has_fulltext":false,"cited_by_count":156,"citation_normalized_percentile":{"value":0.96936684,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"18","issue":"5","first_page":"bbw063","last_page":"bbw063"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":1.0,"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":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":0.9991000294685364,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987999796867371,"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/dna-methylation","display_name":"DNA methylation","score":0.8371682167053223},{"id":"https://openalex.org/keywords/methylation","display_name":"Methylation","score":0.6499911546707153},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.649009644985199},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.6460601091384888},{"id":"https://openalex.org/keywords/cpg-site","display_name":"CpG site","score":0.6251460313796997},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"Carcinogenesis","score":0.6090524196624756},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5503302812576294},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.49977636337280273},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.4556252956390381},{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.4495373070240021},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43146347999572754},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.374680757522583},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3527783751487732},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.2322997748851776},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18312805891036987}],"concepts":[{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.8371682167053223},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.6499911546707153},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.649009644985199},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.6460601091384888},{"id":"https://openalex.org/C140173407","wikidata":"https://www.wikidata.org/wiki/Q1138358","display_name":"CpG site","level":5,"score":0.6251460313796997},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.6090524196624756},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5503302812576294},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.49977636337280273},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.4556252956390381},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.4495373070240021},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43146347999572754},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.374680757522583},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3527783751487732},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.2322997748851776},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18312805891036987}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbw063","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbw063","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:27436122","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27436122","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.75,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":97,"referenced_works":["https://openalex.org/W1533335653","https://openalex.org/W1543156430","https://openalex.org/W1546952499","https://openalex.org/W1547422158","https://openalex.org/W1570622790","https://openalex.org/W1605893472","https://openalex.org/W1769174317","https://openalex.org/W1825543333","https://openalex.org/W1829372799","https://openalex.org/W1910439074","https://openalex.org/W1966322899","https://openalex.org/W1967374891","https://openalex.org/W1967700176","https://openalex.org/W1970856815","https://openalex.org/W1970978490","https://openalex.org/W1971993554","https://openalex.org/W1972954810","https://openalex.org/W1980250100","https://openalex.org/W1981030303","https://openalex.org/W1981196199","https://openalex.org/W1996298672","https://openalex.org/W2000225203","https://openalex.org/W2004543727","https://openalex.org/W2004966039","https://openalex.org/W2007930204","https://openalex.org/W2014140361","https://openalex.org/W2014677321","https://openalex.org/W2019769511","https://openalex.org/W2022152889","https://openalex.org/W2023505669","https://openalex.org/W2027877663","https://openalex.org/W2028640227","https://openalex.org/W2030908134","https://openalex.org/W2032729463","https://openalex.org/W2042568017","https://openalex.org/W2043097295","https://openalex.org/W2046376502","https://openalex.org/W2046710049","https://openalex.org/W2052346441","https://openalex.org/W2054158156","https://openalex.org/W2054286018","https://openalex.org/W2070021921","https://openalex.org/W2070439911","https://openalex.org/W2071821824","https://openalex.org/W2076154138","https://openalex.org/W2079561996","https://openalex.org/W2083162868","https://openalex.org/W2093020414","https://openalex.org/W2094051261","https://openalex.org/W2095924801","https://openalex.org/W2099176640","https://openalex.org/W2100761975","https://openalex.org/W2101870168","https://openalex.org/W2102140136","https://openalex.org/W2104666653","https://openalex.org/W2105032609","https://openalex.org/W2105218532","https://openalex.org/W2107060225","https://openalex.org/W2109281377","https://openalex.org/W2110881699","https://openalex.org/W2117692326","https://openalex.org/W2117792884","https://openalex.org/W2119804413","https://openalex.org/W2124954099","https://openalex.org/W2125342106","https://openalex.org/W2125939156","https://openalex.org/W2126350805","https://openalex.org/W2127192982","https://openalex.org/W2131050852","https://openalex.org/W2134337220","https://openalex.org/W2138057170","https://openalex.org/W2150162153","https://openalex.org/W2161324363","https://openalex.org/W2162080206","https://openalex.org/W2162774116","https://openalex.org/W2165064122","https://openalex.org/W2166186613","https://openalex.org/W2166968390","https://openalex.org/W2179438025","https://openalex.org/W2183336580","https://openalex.org/W2209288790","https://openalex.org/W2252841155","https://openalex.org/W2259938310","https://openalex.org/W2262414037","https://openalex.org/W2329888282","https://openalex.org/W2339740681","https://openalex.org/W2345911841","https://openalex.org/W2400309130","https://openalex.org/W2403309454","https://openalex.org/W2403934794","https://openalex.org/W4206233828","https://openalex.org/W4213257593","https://openalex.org/W4327528266","https://openalex.org/W6636192491","https://openalex.org/W6663914540","https://openalex.org/W6678752534","https://openalex.org/W6712610907"],"related_works":["https://openalex.org/W2902329290","https://openalex.org/W2946746360","https://openalex.org/W2169344098","https://openalex.org/W2139872319","https://openalex.org/W2052355316","https://openalex.org/W2046964473","https://openalex.org/W2107880877","https://openalex.org/W2151182744","https://openalex.org/W2921336251","https://openalex.org/W2944524138"],"abstract_inverted_index":{"Abnormal":[0],"DNA":[1,15,50,60,65,192],"methylation":[2,16,51,61,66,193],"is":[3,18],"an":[4,102],"important":[5],"epigenetic":[6],"regulator":[7],"involving":[8],"tumorigenesis.":[9],"Deciphering":[10],"cancer":[11,56,70,84,137,172,188],"common":[12,57,189],"and":[13,58,85,90,113,131,152,174,185,190],"specific":[14,59,191],"patterns":[17,62],"essential":[19],"for":[20],"us":[21],"to":[22,145],"understand":[23],"the":[24],"mechanisms":[25],"of":[26,39,41,49,68],"tumor":[27,109],"development.":[28],"The":[29],"Cancer":[30],"Genome":[31],"Atlas":[32],"(TCGA)":[33],"project":[34],"provides":[35,181],"a":[36,46,182],"large":[37],"number":[38],"samples":[40],"different":[42],"cancers":[43],"that":[44,142,165],"enable":[45],"pan-cancer":[47,93],"study":[48,180],"possible.":[52],"Here":[53],"we":[54,117,163],"investigate":[55],"among":[63],"5480":[64],"profiles":[67],"15":[69],"types":[71],"from":[72],"TCGA.":[73],"We":[74,139],"first":[75],"define":[76],"differentially":[77],"methylated":[78],"CpG":[79],"sites":[80],"(DMCs)":[81],"in":[82,126,170],"each":[83],"then":[86],"identify":[87,118],"5450":[88],"hyper-":[89,127],"4433":[91],"hypomethylated":[92,129,154],"DMCs":[94,167],"(PDMCs).":[95],"Intriguingly,":[96],"three":[97],"adjacent":[98],"hypermethylated":[99,151],"PDMC":[100],"constitute":[101],"enhancer":[103],"region,":[104],"which":[105,123],"potentially":[106],"regulates":[107],"two":[108],"suppressor":[110],"genes":[111,173],"BVES":[112],"PRDM1":[114],"negatively.":[115],"Moreover,":[116],"six":[119],"distinct":[120,146],"motif":[121],"clusters,":[122],"are":[124,132,156,168],"enriched":[125,169],"or":[128],"PDMCs":[130,143,155],"associated":[133,158],"with":[134,159],"several":[135],"well-known":[136],"hallmarks.":[138],"also":[140],"observe":[141],"relate":[144],"transcriptional":[147],"groups.":[148],"Additionally,":[149],"55":[150],"7":[153],"significantly":[157],"patient":[160],"survival.":[161],"Lastly,":[162],"find":[164],"cancer-specific":[166],"known":[171],"cell-type-specific":[175],"super-enhancers.":[176],"In":[177],"summary,":[178],"this":[179],"comprehensive":[183],"investigation":[184],"reveals":[186],"meaningful":[187],"patterns.":[194]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":32},{"year":2021,"cited_by_count":28},{"year":2020,"cited_by_count":24},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}