{"id":"https://openalex.org/W2947333232","doi":"https://doi.org/10.3233/isb-190472","title":"Lower connectivity of tumor coexpression networks is not specific to cancer","display_name":"Lower connectivity of tumor coexpression networks is not specific to cancer","publication_year":2019,"publication_date":"2019-05-30","ids":{"openalex":"https://openalex.org/W2947333232","doi":"https://doi.org/10.3233/isb-190472","mag":"2947333232","pmid":"https://pubmed.ncbi.nlm.nih.gov/31156157","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/6597990"},"language":"en","primary_location":{"id":"doi:10.3233/isb-190472","doi":"https://doi.org/10.3233/isb-190472","is_oa":true,"landing_page_url":"https://doi.org/10.3233/isb-190472","pdf_url":"https://content.iospress.com:443/download/in-silico-biology/isb190472?id=in-silico-biology%2Fisb190472","source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","medline","norway-1","poland-20","russia-white-list-2"],"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"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":"In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://content.iospress.com:443/download/in-silico-biology/isb190472?id=in-silico-biology%2Fisb190472","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055969196","display_name":"Ertu\u011frul Dalg\u0131\u00e7","orcid":"https://orcid.org/0000-0003-0536-4447","observed_orcids":["https://orcid.org/0000-0003-0536-4447"]},"institutions":[{"id":"https://openalex.org/I3017902709","display_name":"Zonguldak B\u00fclent Ecevit University","ror":"https://ror.org/01dvabv26","country_code":"TR","type":"education","lineage":["https://openalex.org/I3017902709"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Ertu\u011frul Dalg\u0131\u00e7","raw_affiliation_strings":["Department of Medical Biology, Zonguldak B\u00fclent Ecevit University School of Medicine, Zonguldak, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biology, Zonguldak B\u00fclent Ecevit University School of Medicine, Zonguldak, Turkey","institution_ids":["https://openalex.org/I3017902709"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084851102","display_name":"\u00d6zlen Konu","orcid":"https://orcid.org/0000-0002-6223-5329","observed_orcids":["https://orcid.org/0000-0002-6223-5329"]},"institutions":[{"id":"https://openalex.org/I168864056","display_name":"Bilkent University","ror":"https://ror.org/02vh8a032","country_code":"TR","type":"education","lineage":["https://openalex.org/I168864056"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"\u00d6zlen Konu","raw_affiliation_strings":["Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey","institution_ids":["https://openalex.org/I168864056"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025233014","display_name":"Zehra Safi \u00d6z","orcid":"https://orcid.org/0000-0003-1359-5026","observed_orcids":["https://orcid.org/0000-0003-1359-5026"]},"institutions":[{"id":"https://openalex.org/I3017902709","display_name":"Zonguldak B\u00fclent Ecevit University","ror":"https://ror.org/01dvabv26","country_code":"TR","type":"education","lineage":["https://openalex.org/I3017902709"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Zehra Safi \u00d6z","raw_affiliation_strings":["Department of Medical Biology, Zonguldak B\u00fclent Ecevit University School of Medicine, Zonguldak, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medical Biology, Zonguldak B\u00fclent Ecevit University School of Medicine, Zonguldak, Turkey","institution_ids":["https://openalex.org/I3017902709"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102757744","display_name":"Christina Chan","orcid":"https://orcid.org/0000-0003-3054-2727","observed_orcids":["https://orcid.org/0000-0003-3054-2727","https://orcid.org/0009-0003-7693-8206"]},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christina Chan","raw_affiliation_strings":["Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA","E-mail:","Fax: +90 3722610264"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA","institution_ids":["https://openalex.org/I87216513"]},{"raw_affiliation_string":"E-mail:","institution_ids":[]},{"raw_affiliation_string":"Fax: +90 3722610264","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5055969196"],"corresponding_institution_ids":["https://openalex.org/I3017902709"],"apc_list":null,"apc_paid":null,"fwci":0.4961,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58386279,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"13","issue":"1-2","first_page":"41","last_page":"53"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9804999828338623,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9804999828338623,"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":0.016300000250339508,"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":0.0006000000284984708,"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/gene-co-expression-network","display_name":"gene co-expression network","score":0.8989999890327454},{"id":"https://openalex.org/keywords/network-connectivity","display_name":"network connectivity","score":0.9210000038146973},{"id":"https://openalex.org/keywords/colorectal-adenoma","display_name":"colorectal adenoma","score":0.9399999976158142},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"colorectal cancer","score":0.953000009059906},{"id":"https://openalex.org/keywords/aldosterone-producing-adenoma","display_name":"aldosterone-producing adenoma","score":0.9330000281333923},{"id":"https://openalex.org/keywords/uterine-fibroids","display_name":"uterine fibroids","score":1.0},{"id":"https://openalex.org/keywords/hub-genes","display_name":"hub genes","score":0.8100000023841858},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.6840000152587891},{"id":"https://openalex.org/keywords/extracellular-space","display_name":"extracellular space","score":0.8600000143051147},{"id":"https://openalex.org/keywords/malignant-transformation","display_name":"malignant transformation","score":0.47099998593330383},{"id":"https://openalex.org/keywords/network-topology","display_name":"network topology","score":0.30399999022483826}],"concepts":[{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.6650212407112122},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5817577242851257},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5746989846229553},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5298348069190979},{"id":"https://openalex.org/C33288867","wikidata":"https://www.wikidata.org/wiki/Q518328","display_name":"Methylation","level":3,"score":0.5236691832542419},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.4864192008972168},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45077869296073914},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.43453699350357056},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.4302785098552704},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26748815178871155},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07681655883789062},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009928","descriptor_name":"Organ Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060787","descriptor_name":"Neoplasm Grading","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.3233/isb-190472","doi":"https://doi.org/10.3233/isb-190472","is_oa":true,"landing_page_url":"https://doi.org/10.3233/isb-190472","pdf_url":"https://content.iospress.com:443/download/in-silico-biology/isb190472?id=in-silico-biology%2Fisb190472","source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","medline","norway-1","poland-20","russia-white-list-2"],"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"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":"In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6597990","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6597990","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"In Silico Biol","raw_type":"Text"},{"id":"pmid:31156157","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31156157","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":"In silico biology","raw_type":"Journal Article"},{"id":"pmh:oai:repository.bilkent.edu.tr:11693/53145","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/11693/53145","pdf_url":"https://repository.bilkent.edu.tr/bitstreams/ed262b5e-de2d-401b-9872-a7d3d6a7b5e0/download","source":{"id":"https://openalex.org/S4306400079","display_name":"Bilkent University Institutional Repository (Bilkent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I168864056","host_organization_name":"Bilkent University","host_organization_lineage":["https://openalex.org/I168864056"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"In Silico Biology","raw_type":"Article"},{"id":"pmh:oai:acikarsiv.beun.edu.tr:20.500.12628/24835","doi":null,"is_oa":false,"landing_page_url":"https://hdl.handle.net/20.500.12628/24835","pdf_url":null,"source":{"id":"https://openalex.org/S7407055168","display_name":"Zonguldak B\u00fclent Ecevit University Institutional Repository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"Article"}],"best_oa_location":{"id":"doi:10.3233/isb-190472","doi":"https://doi.org/10.3233/isb-190472","is_oa":true,"landing_page_url":"https://doi.org/10.3233/isb-190472","pdf_url":"https://content.iospress.com:443/download/in-silico-biology/isb190472?id=in-silico-biology%2Fisb190472","source":{"id":"https://openalex.org/S120694666","display_name":"In Silico Biology","issn_l":"1386-6338","issn":["1386-6338","1434-3207"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","jufo-1","medline","norway-1","poland-20","russia-white-list-2"],"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"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":"In Silico Biology: Journal of Biological Systems Modeling and Multi-Scale Simulation","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.9537000060081482}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322626","display_name":"T\u00fcrkiye Bilimsel ve Teknolojik Ara\u015ft\u0131rma Kurumu","ror":"https://ror.org/04w9kkr77"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2947333232.pdf","grobid_xml":"https://content.openalex.org/works/W2947333232.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1559908735","https://openalex.org/W1984292058","https://openalex.org/W2039664374","https://openalex.org/W2088479878","https://openalex.org/W2100025044","https://openalex.org/W2102140136","https://openalex.org/W2108539496","https://openalex.org/W2112947018","https://openalex.org/W2116634113","https://openalex.org/W2133465414","https://openalex.org/W2136479434","https://openalex.org/W2142720308","https://openalex.org/W2158217645","https://openalex.org/W2159675211","https://openalex.org/W2170989872","https://openalex.org/W2171115585","https://openalex.org/W2534924637","https://openalex.org/W2952606899","https://openalex.org/W3022936582"],"related_works":["https://openalex.org/W2039664374","https://openalex.org/W4249558049","https://openalex.org/W2947213478","https://openalex.org/W7131309848","https://openalex.org/W3214798941","https://openalex.org/W1559908735","https://openalex.org/W1984292058","https://openalex.org/W7149385005","https://openalex.org/W2998585468","https://openalex.org/W4296121857"],"abstract_inverted_index":{"Global":[0],"level":[1,11,185,203],"network":[2,50],"analysis":[3],"of":[4,13,31,54,61,83,101,146,151,177,187,212],"molecular":[5],"links":[6],"is":[7,104],"necessary":[8],"for":[9,45,86],"systems":[10,184,202],"view":[12],"complex":[14],"diseases":[15],"like":[16],"cancer.":[17],"Using":[18],"genome-wide":[19],"expression":[20],"datasets,":[21],"we":[22,65],"constructed":[23],"and":[24,35,92,173],"compared":[25],"gene":[26,136],"co-expression":[27],"based":[28,112,170],"specific":[29,106,148],"networks":[30,42],"pre-cancerous":[32,68,199],"tumors":[33,37],"(adenoma)":[34],"cancerous":[36],"(carcinoma)":[38],"with":[39],"paired":[40,76],"normal":[41,77],"to":[43,107,193,209],"assess":[44],"any":[46],"possible":[47],"changes":[48],"in":[49,126,167],"connectivity.":[51],"Previously,":[52],"loss":[53,82,100],"connectivity":[55,84,102,145,189],"was":[56,156],"reported":[57],"as":[58,190],"a":[59,81,183,210],"characteristics":[60],"cancer":[62,153,196],"samples.":[63,78],"Here,":[64],"observed":[66,80],"that":[67,98],"conditions":[69],"also":[70,96,198],"had":[71],"significantly":[72],"less":[73,123],"connections":[74],"than":[75],"We":[79,95],"trend":[85,103],"colorectal":[87,152,178],"adenoma,":[88],"aldosterone":[89],"producing":[90],"adenoma":[91],"uterine":[93],"leiomyoma.":[94],"showed":[97],"the":[99,119,143],"not":[105,194,206],"positive":[108],"or":[109],"negative":[110,168],"correlation":[111,169],"networks.":[113,149],"Differential":[114],"hub":[115],"genes,":[116],"which":[117,141],"were":[118,128,165],"most":[120],"highly":[121],"differentially":[122],"connected":[124],"genes":[125],"tumor,":[127],"mostly":[129],"different":[130,132,157],"between":[131],"datasets.":[133],"No":[134],"common":[135,174],"list":[137],"could":[138,205],"be":[139,207],"defined":[140],"underlies":[142],"lower":[144,188],"tumor":[147],"Connectivity":[150],"methylation":[154,175],"targets":[155,176],"from":[158],"other":[159],"genes.":[160,213],"Extracellular":[161],"space":[162],"related":[163],"terms":[164],"enriched":[166],"differential":[171],"hubs":[172],"carcinoma.":[179],"Our":[180],"results":[181],"indicate":[182],"change":[186],"cells":[191],"transform":[192],"only":[195],"but":[197],"conditions.":[200],"This":[201],"behavior":[204],"attributed":[208],"group":[211]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2019-06-07T00:00:00"}