{"id":"https://openalex.org/W2149060064","doi":"https://doi.org/10.1186/1752-0509-6-65","title":"Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases","display_name":"Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases","publication_year":2012,"publication_date":"2012-06-13","ids":{"openalex":"https://openalex.org/W2149060064","doi":"https://doi.org/10.1186/1752-0509-6-65","mag":"2149060064","pmid":"https://pubmed.ncbi.nlm.nih.gov/22694839"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-65","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-65","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-65","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-65","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100345976","display_name":"Yu Liu","orcid":"https://orcid.org/0009-0007-6599-5685"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yu Liu","raw_affiliation_strings":["Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA. yxl442@case.edu","Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA. yxl442@case.edu","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035558591","display_name":"Mehmet Koyut\u00fcrk","orcid":"https://orcid.org/0000-0002-3434-5512"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mehmet Koyut\u00fcrk","raw_affiliation_strings":["Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA","Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, USA","Department of Electrical Engineering & Computer Science, Case Western Reserve University, Cleveland, OH, 44106, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Department of Electrical Engineering & Computer Science, Case Western Reserve University, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051948022","display_name":"Jill S. Barnholtz\u2010Sloan","orcid":"https://orcid.org/0000-0001-6190-9304"},"institutions":[{"id":"https://openalex.org/I4210108791","display_name":"University Hospitals Cleveland Medical Center","ror":"https://ror.org/01gc0wp38","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799343972","https://openalex.org/I4210108791"]},{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jill S Barnholtz-Sloan","raw_affiliation_strings":["Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA","Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, USA","Department of Epidemiology and Biostatistics, Case Comprehensive Cancer Center, Cleveland, OH, 44106, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, Case Comprehensive Cancer Center, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I4210108791"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071940002","display_name":"Mark R. Chance","orcid":"https://orcid.org/0000-0002-2991-6405"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark R Chance","raw_affiliation_strings":["Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA","Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, USA","Department of Genetics, Case Western Reserve University, Cleveland, OH, 44106, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Center for Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Department of Genetics, Case Western Reserve University, Cleveland, OH, 44106, USA","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100345976"],"corresponding_institution_ids":["https://openalex.org/I58956616"],"apc_list":null,"apc_paid":null,"fwci":2.5525,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.90052672,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"6","issue":"1","first_page":"65","last_page":"65"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9846000075340271,"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":0.9846000075340271,"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":0.002899999963119626,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.0027000000700354576,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.71653151512146},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6528874635696411},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6155585050582886},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.567694365978241},{"id":"https://openalex.org/keywords/gene-interaction","display_name":"Gene interaction","score":0.5409234166145325},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5387628078460693},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.5261311531066895},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5118574500083923},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.49773409962654114},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.494549959897995},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.4908669590950012},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4578148424625397},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.41481274366378784},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31431275606155396}],"concepts":[{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.71653151512146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6528874635696411},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6155585050582886},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.567694365978241},{"id":"https://openalex.org/C2991772755","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Gene interaction","level":3,"score":0.5409234166145325},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5387628078460693},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.5261311531066895},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5118574500083923},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.49773409962654114},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.494549959897995},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.4908669590950012},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4578148424625397},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.41481274366378784},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31431275606155396},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004194","descriptor_name":"Disease","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004843","descriptor_name":"Epistasis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004843","descriptor_name":"Epistasis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004843","descriptor_name":"Epistasis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004843","descriptor_name":"Epistasis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004843","descriptor_name":"Epistasis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D009154","descriptor_name":"Mutation","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":"D009154","descriptor_name":"Mutation","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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016159","descriptor_name":"Tumor Suppressor Protein p53","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051025","descriptor_name":"bcl-Associated Death Protein","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051025","descriptor_name":"bcl-Associated Death Protein","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051025","descriptor_name":"bcl-Associated Death Protein","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051025","descriptor_name":"bcl-Associated Death Protein","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D051025","descriptor_name":"bcl-Associated Death Protein","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/1752-0509-6-65","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-65","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-65","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:22694839","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22694839","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:commons.case.edu:facultyworks-1841","is_oa":true,"landing_page_url":"https://commons.case.edu/facultyworks/838","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Scholarship","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:fff9d8e280bd4288b30d806eb7afe06f","is_oa":false,"landing_page_url":"https://doaj.org/article/fff9d8e280bd4288b30d806eb7afe06f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":"BMC Systems Biology, Vol 6, Iss 1, p 65 (2012)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3426489","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3426489","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,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Syst Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-65","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-65","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-65","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5400000214576721,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G1708576474","display_name":null,"funder_award_id":"UL1 RR024989","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G1853179733","display_name":null,"funder_award_id":"UL1 RR024989","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4349461467","display_name":null,"funder_award_id":"UL1 RR024989","funder_id":"https://openalex.org/F4320310281","funder_display_name":"Case Western Reserve University"},{"id":"https://openalex.org/G4398992664","display_name":null,"funder_award_id":"IIS-0916102","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5534187794","display_name":null,"funder_award_id":"RR024989","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G555309615","display_name":"III: Small: Computational Infrastructure for the Identification of Copy Number Variations from SNP Microarrays","funder_award_id":"0916102","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5822270753","display_name":null,"funder_award_id":"CA043703","funder_id":"https://openalex.org/F4320310595","funder_display_name":"Case Comprehensive Cancer Center, Case Western Reserve University"},{"id":"https://openalex.org/G8183162102","display_name":null,"funder_award_id":"UL1 RR024989","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8225734366","display_name":null,"funder_award_id":"RR024989","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G8543032451","display_name":null,"funder_award_id":"CA043703","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309680","display_name":"Cleveland Clinic","ror":"https://ror.org/03xjacd83"},{"id":"https://openalex.org/F4320310281","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666"},{"id":"https://openalex.org/F4320310595","display_name":"Case Comprehensive Cancer Center, Case Western Reserve University","ror":"https://ror.org/051fd9666"},{"id":"https://openalex.org/F4320316438","display_name":"Georgia Clinical and Translational Science Alliance","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2149060064.pdf","grobid_xml":"https://content.openalex.org/works/W2149060064.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1539800059","https://openalex.org/W1558961953","https://openalex.org/W1964895626","https://openalex.org/W1965055200","https://openalex.org/W1965488058","https://openalex.org/W1973821009","https://openalex.org/W1977918192","https://openalex.org/W1980175560","https://openalex.org/W1982203054","https://openalex.org/W1987922405","https://openalex.org/W1993362565","https://openalex.org/W1995594551","https://openalex.org/W2002244693","https://openalex.org/W2002505993","https://openalex.org/W2002936090","https://openalex.org/W2003924241","https://openalex.org/W2018843280","https://openalex.org/W2020859582","https://openalex.org/W2022756191","https://openalex.org/W2031100365","https://openalex.org/W2049203095","https://openalex.org/W2073576377","https://openalex.org/W2082430676","https://openalex.org/W2087800278","https://openalex.org/W2088477148","https://openalex.org/W2098864059","https://openalex.org/W2101933440","https://openalex.org/W2107040525","https://openalex.org/W2119371482","https://openalex.org/W2129221351","https://openalex.org/W2130410032","https://openalex.org/W2133102806","https://openalex.org/W2135772170","https://openalex.org/W2138155367","https://openalex.org/W2141122392","https://openalex.org/W2142183096","https://openalex.org/W2146997276","https://openalex.org/W2151936673","https://openalex.org/W2152667098","https://openalex.org/W2154947819","https://openalex.org/W2158823426","https://openalex.org/W2164050296","https://openalex.org/W2168264491","https://openalex.org/W2169576771","https://openalex.org/W2364425459","https://openalex.org/W6632453849"],"related_works":["https://openalex.org/W2158714033","https://openalex.org/W2163262592","https://openalex.org/W3213185671","https://openalex.org/W4210989272","https://openalex.org/W4206945140","https://openalex.org/W4386628104","https://openalex.org/W78967844","https://openalex.org/W2127864418","https://openalex.org/W2140469676","https://openalex.org/W2161484887"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,35,184],"molecular":[2],"behavior":[3],"of":[4,12,30,48,51,86,89,99,113,140,160,163,173,178,211,214,232,264,272,276],"biological":[5,209],"systems":[6,225],"can":[7,41],"be":[8,42],"described":[9],"in":[10,45,56,65,193],"terms":[11],"three":[13],"fundamental":[14],"components:":[15],"(i)":[16],"the":[17,21,28,46,49,62,90,97,100,155,181,208,220,224,230,257,273,282,297],"physical":[18],"entities,":[19,25],"(ii)":[20],"interactions":[22,101,159,189,198,283],"among":[23,180],"these":[24,31,52],"and":[26,33,77,116,129,147,190,204,261,292,302],"(iii)":[27],"dynamics":[29,98],"entities":[32,91],"interactions.":[34],"mechanisms":[36],"that":[37,199,243,248,262],"drive":[38],"complex":[39],"disease":[40,105,146],"productively":[43],"viewed":[44],"context":[47],"perturbations":[50],"components.":[53],"One":[54],"challenge":[55],"this":[57,70],"regard":[58],"is":[59],"to":[60,104,133,153,238],"identify":[61,134],"pathways":[63,191,247,294],"altered":[64],"specific":[66,287],"diseases.":[67],"To":[68],"address":[69],"challenge,":[71],"Gene":[72,126],"Set":[73],"Enrichment":[74,128],"Analysis":[75,131],"(GSEA)":[76],"others":[78],"have":[79,106],"been":[80,107],"developed,":[81],"which":[82],"focus":[83],"on":[84,207,256],"alterations":[85],"individual":[87,258],"properties":[88,112,260],"(such":[92],"as":[93],"gene":[94,136,158,259,288],"expression).":[95],"However,":[96],"with":[102,268,296],"respect":[103],"less":[108],"well":[109],"studied":[110],"(i.e.,":[111],"components":[114],"ii":[115],"iii).":[117],"RESULTS:":[118],"Here,":[119],"we":[120],"present":[121],"a":[122],"novel":[123],"method":[124],"called":[125],"Interaction":[127],"Network":[130],"(GIENA)":[132],"dysregulated":[135,188,194,215,246],"interactions,":[137],"i.e.,":[138],"pairs":[139],"genes":[141],"whose":[142],"relationships":[143],"differ":[144],"between":[145,168],"control.":[148],"Four":[149],"functions":[150],"are":[151,200,249,300],"defined":[152],"model":[154],"biologically":[156],"relevant":[157,277,298],"cooperation":[161],"(sum":[162],"mRNA":[164,169],"expression),":[165,170,174],"competition":[166],"(difference":[167],"redundancy":[171],"(maximum":[172],"or":[175],"dependency":[176],"(minimum":[177],"expression)":[179],"expression":[182],"levels.":[183],"proposed":[185],"framework":[186],"identifies":[187,245],"enriched":[192],"interactions;":[195],"points":[196],"out":[197],"perturbed":[201],"across":[202,293],"pathways;":[203],"moreover,":[205],"based":[206,255],"annotation":[210],"each":[212],"type":[213],"interaction":[216],"gives":[217],"clues":[218],"about":[219],"regulatory":[221],"logic":[222],"governing":[223],"level":[226],"perturbation.":[227],"We":[228,241],"demonstrated":[229],"potential":[231],"GIENA":[233,244,269],"using":[234,281],"published":[235],"datasets":[236],"related":[237],"cancer.":[239],"CONCLUSIONS:":[240],"showed":[242],"missed":[250],"by":[251,285],"traditional":[252,265],"enrichment":[253],"methods":[254,266],"use":[263],"combined":[267],"provides":[270],"coverage":[271],"largest":[274],"number":[275],"pathways.":[278],"In":[279],"addition,":[280],"detected":[284],"GIENA,":[286],"networks":[289],"both":[290],"within":[291],"associated":[295],"phenotypes":[299],"constructed":[301],"analyzed.":[303]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
