{"id":"https://openalex.org/W2810690816","doi":"https://doi.org/10.3748/wjg.v24.i24.2605","title":"Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma","display_name":"Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma","publication_year":2018,"publication_date":"2018-06-25","ids":{"openalex":"https://openalex.org/W2810690816","doi":"https://doi.org/10.3748/wjg.v24.i24.2605","mag":"2810690816","pmid":"https://pubmed.ncbi.nlm.nih.gov/29962817","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/6021769"},"language":"en","primary_location":{"id":"doi:10.3748/wjg.v24.i24.2605","doi":"https://doi.org/10.3748/wjg.v24.i24.2605","is_oa":true,"landing_page_url":"https://doi.org/10.3748/wjg.v24.i24.2605","pdf_url":null,"source":{"id":"https://openalex.org/S181459644","display_name":"World Journal of Gastroenterology","issn_l":"1007-9327","issn":["1007-9327","2219-2840"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","poland-100","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315735","host_organization_name":"Baishideng Publishing Group","host_organization_lineage":["https://openalex.org/P4310315735"],"host_organization_lineage_names":["Baishideng Publishing Group"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"World Journal of Gastroenterology","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.3748/wjg.v24.i24.2605","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103233383","display_name":"Liang Sang","orcid":"https://orcid.org/0000-0002-9331-0985","observed_orcids":["https://orcid.org/0000-0002-9331-0985"]},"institutions":[{"id":"https://openalex.org/I4210140515","display_name":"First Hospital of China Medical University","ror":"https://ror.org/04wjghj95","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210140515"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Sang","raw_affiliation_strings":["Department of Ultrasound, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ultrasound, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China","institution_ids":["https://openalex.org/I4210140515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100390607","display_name":"Xuemei Wang","orcid":"https://orcid.org/0000-0002-3516-0966","observed_orcids":["https://orcid.org/0000-0002-3516-0966"]},"institutions":[{"id":"https://openalex.org/I4210140515","display_name":"First Hospital of China Medical University","ror":"https://ror.org/04wjghj95","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210140515"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xue-Mei Wang","raw_affiliation_strings":["Department of Ultrasound, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China. wangxuemei@cmu1h.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ultrasound, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China. wangxuemei@cmu1h.com","institution_ids":["https://openalex.org/I4210140515"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100734235","display_name":"Dongyang Xu","orcid":"https://orcid.org/0000-0001-7071-9764","observed_orcids":["https://orcid.org/0000-0001-7071-9764"]},"institutions":[{"id":"https://openalex.org/I4210140515","display_name":"First Hospital of China Medical University","ror":"https://ror.org/04wjghj95","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210140515"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong-Yang Xu","raw_affiliation_strings":["Department of Ultrasound, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ultrasound, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China","institution_ids":["https://openalex.org/I4210140515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101963654","display_name":"Wenjing Zhao","orcid":"https://orcid.org/0000-0003-4477-596X","observed_orcids":["https://orcid.org/0000-0003-4477-596X"]},"institutions":[{"id":"https://openalex.org/I4210140515","display_name":"First Hospital of China Medical University","ror":"https://ror.org/04wjghj95","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210140515"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen-Jing Zhao","raw_affiliation_strings":["Department of Ultrasound, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Ultrasound, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China","institution_ids":["https://openalex.org/I4210140515"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210140515"],"apc_list":null,"apc_paid":null,"fwci":3.4341,"has_fulltext":true,"cited_by_count":66,"citation_normalized_percentile":{"value":0.94417935,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"24","issue":"24","first_page":"2605","last_page":"2616"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10269","display_name":"Epigenetics and DNA Methylation","score":0.4530999958515167,"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":0.4530999958515167,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.21690000593662262,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.15520000457763672,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/hepatocellular-carcinoma","display_name":"hepatocellular carcinoma","score":1.0},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.8939999938011169},{"id":"https://openalex.org/keywords/differentially-methylated-genes","display_name":"differentially methylated genes","score":0.9490000009536743},{"id":"https://openalex.org/keywords/differentially-expressed-genes","display_name":"differentially expressed genes","score":0.9869999885559082},{"id":"https://openalex.org/keywords/hub-genes","display_name":"hub genes","score":0.8550000190734863},{"id":"https://openalex.org/keywords/protein-protein-interaction-network","display_name":"protein-protein interaction network","score":0.984000027179718},{"id":"https://openalex.org/keywords/functional-enrichment-analysis","display_name":"functional enrichment","score":0.5360000133514404},{"id":"https://openalex.org/keywords/biomarkers","display_name":"biomarkers","score":0.8009999990463257}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7491902709007263},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.672425389289856},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.5758593678474426},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5566059947013855},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.5289962887763977},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5141565799713135},{"id":"https://openalex.org/C29537977","wikidata":"https://www.wikidata.org/wiki/Q188941","display_name":"Cell cycle","level":3,"score":0.48838919401168823},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46977370977401733},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.4317072629928589},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.4214783310890198},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.320594847202301},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3164583742618561}],"mesh":[{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006528","descriptor_name":"Carcinoma, Hepatocellular","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D008113","descriptor_name":"Liver Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","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":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D066264","descriptor_name":"Datasets as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.3748/wjg.v24.i24.2605","doi":"https://doi.org/10.3748/wjg.v24.i24.2605","is_oa":true,"landing_page_url":"https://doi.org/10.3748/wjg.v24.i24.2605","pdf_url":null,"source":{"id":"https://openalex.org/S181459644","display_name":"World Journal of Gastroenterology","issn_l":"1007-9327","issn":["1007-9327","2219-2840"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","poland-100","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315735","host_organization_name":"Baishideng Publishing Group","host_organization_lineage":["https://openalex.org/P4310315735"],"host_organization_lineage_names":["Baishideng Publishing Group"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"World Journal of Gastroenterology","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6021769","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC6021769/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC6021769/pdf/","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,"listed_in":[],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"World J Gastroenterol","raw_type":"Text"},{"id":"pmh:oai:europepmc.org:4972332","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6021769","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,"listed_in":[],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"},{"id":"pmid:29962817","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29962817","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,"listed_in":[],"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":"World journal of gastroenterology","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.3748/wjg.v24.i24.2605","doi":"https://doi.org/10.3748/wjg.v24.i24.2605","is_oa":true,"landing_page_url":"https://doi.org/10.3748/wjg.v24.i24.2605","pdf_url":null,"source":{"id":"https://openalex.org/S181459644","display_name":"World Journal of Gastroenterology","issn_l":"1007-9327","issn":["1007-9327","2219-2840"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","poland-100","russia-white-list-1"],"host_organization":"https://openalex.org/P4310315735","host_organization_name":"Baishideng Publishing Group","host_organization_lineage":["https://openalex.org/P4310315735"],"host_organization_lineage_names":["Baishideng Publishing Group"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"World Journal of Gastroenterology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.9391000270843506,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2810690816.pdf","grobid_xml":"https://content.openalex.org/works/W2810690816.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1856975046","https://openalex.org/W1956418068","https://openalex.org/W1989557556","https://openalex.org/W1994564728","https://openalex.org/W1996592551","https://openalex.org/W2013057597","https://openalex.org/W2021753885","https://openalex.org/W2022495797","https://openalex.org/W2023191100","https://openalex.org/W2029097932","https://openalex.org/W2032809798","https://openalex.org/W2046591786","https://openalex.org/W2047941151","https://openalex.org/W2069717224","https://openalex.org/W2078879586","https://openalex.org/W2085434377","https://openalex.org/W2099887488","https://openalex.org/W2125040419","https://openalex.org/W2125479243","https://openalex.org/W2140446354","https://openalex.org/W2144520068","https://openalex.org/W2158217645","https://openalex.org/W2159482845","https://openalex.org/W2226973512","https://openalex.org/W2300466696","https://openalex.org/W2328467730","https://openalex.org/W2410637760","https://openalex.org/W2421111122","https://openalex.org/W2473228288","https://openalex.org/W2487261336","https://openalex.org/W2512939027","https://openalex.org/W2525359987","https://openalex.org/W2529532071","https://openalex.org/W2531825134","https://openalex.org/W2535137796","https://openalex.org/W2598645546","https://openalex.org/W2604279563","https://openalex.org/W2611216326","https://openalex.org/W2613316333","https://openalex.org/W2729416070","https://openalex.org/W2738055411","https://openalex.org/W2738103349","https://openalex.org/W2772282916","https://openalex.org/W2772389618","https://openalex.org/W2786042945","https://openalex.org/W2917837889","https://openalex.org/W4231824804","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W3134203423","https://openalex.org/W4210310163","https://openalex.org/W2890534939","https://openalex.org/W3087162760","https://openalex.org/W4283589494","https://openalex.org/W2910511485","https://openalex.org/W2755775219","https://openalex.org/W3122676370","https://openalex.org/W4307136493","https://openalex.org/W4283643136"],"abstract_inverted_index":{"AIM:":[0],"To":[1],"discover":[2],"methylated-differentially":[3],"expressed":[4,44],"genes":[5,16,41,45,76,99],"(MDEGs)":[6],"in":[7,73,93],"hepatocellular":[8],"carcinoma":[9],"(HCC)":[10],"and":[11,17,27,42,50,70,81,124],"to":[12],"explore":[13],"relevant":[14],"hub":[15,98],"potential":[18],"pathways.":[19],"METHODS:":[20],"The":[21],"data":[22],"of":[23,53,85,107,126],"expression":[24],"profiling":[25,29],"GSE25097":[26],"methylation":[28,119],"GSE57956":[30],"were":[31,55,77,97],"gained":[32],"from":[33],"GEO":[34],"Datasets.":[35],"We":[36],"analyzed":[37],"the":[38,58,86,121],"differentially":[39,43],"methylated":[40],"online":[46],"using":[47,57],"GEO2R.":[48],"Functional":[49],"enrichment":[51],"analyses":[52],"MDEGs":[54],"conducted":[56,90],"DAVID":[59],"database.":[60],"A":[61],"protein-protein":[62],"interaction":[63],"(PPI)":[64],"network":[65,88],"was":[66,89],"performed":[67],"by":[68,79,91,102],"STRING":[69],"then":[71],"visualized":[72],"Cytoscape.":[74],"Hub":[75],"ranked":[78,105],"cytoHubba,":[80],"a":[82],"module":[83],"analysis":[84],"PPI":[87],"MCODE":[92],"Cytoscape":[94],"software.":[95],"RESULTS:":[96],"for":[100,120],"Hypo-HGs":[101],"combining":[103],"six":[104],"methods":[106],"cytoHubba.":[108],"CONCLUSION:":[109],",":[110],"can":[111],"be":[112],"used":[113],"as":[114],"biomarkers":[115],"based":[116],"on":[117],"aberrant":[118],"accurate":[122],"diagnosis":[123],"treatment":[125],"HCC.":[127]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":19},{"year":2019,"cited_by_count":11},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1}],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2018-07-10T00:00:00"}
