{"id":"https://openalex.org/W2114439422","doi":"https://doi.org/10.1186/1752-0509-6-s2-s12","title":"Computational gene network analysis reveals TNF-induced angiogenesis","display_name":"Computational gene network analysis reveals TNF-induced angiogenesis","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W2114439422","doi":"https://doi.org/10.1186/1752-0509-6-s2-s12","mag":"2114439422","pmid":"https://pubmed.ncbi.nlm.nih.gov/23281897"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-6-s2-s12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s2-s12","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S2-S12","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S2-S12","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113846429","display_name":"Kentaro Ogami","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kentaro Ogami","raw_affiliation_strings":["Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 Japan","Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo 108-8639, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-Ku, Tokyo 108-8639, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078146127","display_name":"Rui Yamaguchi","orcid":"https://orcid.org/0000-0003-1224-227X"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Rui Yamaguchi","raw_affiliation_strings":["Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai Minato-ku, Tokyo, 108-8639, Japan","Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai Minato-ku, Tokyo, 108-8639, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090788230","display_name":"Seiya Imoto","orcid":"https://orcid.org/0000-0002-2989-308X"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Seiya Imoto","raw_affiliation_strings":["Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai Minato-ku, Tokyo, 108-8639, Japan","Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai Minato-ku, Tokyo, 108-8639, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088441205","display_name":"Yoshinori Tamada","orcid":"https://orcid.org/0000-0003-3483-9712"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshinori Tamada","raw_affiliation_strings":["Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan","Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, 7-3-1Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokyo, Japan#TAB#","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068206232","display_name":"Hiromitsu Araki","orcid":null},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Hiromitsu Araki","raw_affiliation_strings":["Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand","Department of Molecular Medicine & Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand","institution_ids":["https://openalex.org/I154130895"]},{"raw_affiliation_string":"Department of Molecular Medicine & Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064023142","display_name":"Cristin G. Print","orcid":"https://orcid.org/0000-0001-8345-7812"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Cristin Print","raw_affiliation_strings":["Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand","Department of Molecular Medicine & Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand","institution_ids":["https://openalex.org/I154130895"]},{"raw_affiliation_string":"Department of Molecular Medicine & Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088167618","display_name":"Satoru Miyano","orcid":"https://orcid.org/0000-0002-1753-6616"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Satoru Miyano","raw_affiliation_strings":["Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai Minato-ku, Tokyo, 108-8639, Japan","Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai Minato-ku, Tokyo, 108-8639, Japan","institution_ids":["https://openalex.org/I74801974"]},{"raw_affiliation_string":"Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5088167618"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":1.353,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.79894554,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"6","issue":"S2","first_page":"S12","last_page":"S12"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.545799970626831,"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":0.545799970626831,"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":0.15119999647140503,"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/T10422","display_name":"Angiogenesis and VEGF in Cancer","score":0.022199999541044235,"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/angiogenesis","display_name":"Angiogenesis","score":0.90477454662323},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5785360932350159},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5709839463233948},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5621926784515381},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5314691662788391},{"id":"https://openalex.org/keywords/tumor-necrosis-factor-alpha","display_name":"Tumor necrosis factor alpha","score":0.5158602595329285},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.49802327156066895},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4938279092311859},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4844991862773895},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.4692136347293854},{"id":"https://openalex.org/keywords/interleukin-8","display_name":"Interleukin 8","score":0.4363536834716797},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.373900830745697},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.3054140508174896},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2938600480556488},{"id":"https://openalex.org/keywords/cytokine","display_name":"Cytokine","score":0.15817496180534363}],"concepts":[{"id":"https://openalex.org/C2780394083","wikidata":"https://www.wikidata.org/wiki/Q539568","display_name":"Angiogenesis","level":2,"score":0.90477454662323},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5785360932350159},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5709839463233948},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5621926784515381},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5314691662788391},{"id":"https://openalex.org/C17991360","wikidata":"https://www.wikidata.org/wiki/Q21173843","display_name":"Tumor necrosis factor alpha","level":2,"score":0.5158602595329285},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.49802327156066895},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4938279092311859},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4844991862773895},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.4692136347293854},{"id":"https://openalex.org/C68324877","wikidata":"https://www.wikidata.org/wiki/Q421859","display_name":"Interleukin 8","level":3,"score":0.4363536834716797},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.373900830745697},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.3054140508174896},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2938600480556488},{"id":"https://openalex.org/C2778690821","wikidata":"https://www.wikidata.org/wiki/Q212354","display_name":"Cytokine","level":2,"score":0.15817496180534363}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","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":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D014409","descriptor_name":"Tumor Necrosis Factor-alpha","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018919","descriptor_name":"Neovascularization, Physiologic","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D018919","descriptor_name":"Neovascularization, Physiologic","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D018919","descriptor_name":"Neovascularization, Physiologic","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D018919","descriptor_name":"Neovascularization, Physiologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018919","descriptor_name":"Neovascularization, Physiologic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018919","descriptor_name":"Neovascularization, Physiologic","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":"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":"D061307","descriptor_name":"Human Umbilical Vein Endothelial Cells","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D061307","descriptor_name":"Human Umbilical Vein Endothelial Cells","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D061307","descriptor_name":"Human Umbilical Vein Endothelial Cells","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D061307","descriptor_name":"Human Umbilical Vein Endothelial Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D061307","descriptor_name":"Human Umbilical Vein Endothelial Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D061307","descriptor_name":"Human Umbilical Vein Endothelial Cells","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-6-s2-s12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s2-s12","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S2-S12","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:23281897","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23281897","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2521547","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3521175","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,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-6-s2-s12","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-6-s2-s12","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-6-S2-S12","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":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.7300000190734863}],"awards":[{"id":"https://openalex.org/G4747599023","display_name":"Development of methods to extact kowledge from drug-stimulated gene expression time-coure compendium data","funder_award_id":"24700292","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320336716","display_name":"Institute of Medical Science, University of Tokyo","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2114439422.pdf","grobid_xml":"https://content.openalex.org/works/W2114439422.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W102419489","https://openalex.org/W153837530","https://openalex.org/W1564674105","https://openalex.org/W1641228030","https://openalex.org/W1965334406","https://openalex.org/W1985147506","https://openalex.org/W1992899791","https://openalex.org/W2029604887","https://openalex.org/W2044605749","https://openalex.org/W2050019055","https://openalex.org/W2089478514","https://openalex.org/W2122683221","https://openalex.org/W2133986577","https://openalex.org/W2138515833","https://openalex.org/W2146053439","https://openalex.org/W2149932234","https://openalex.org/W2155872278","https://openalex.org/W2164130043","https://openalex.org/W2318758727","https://openalex.org/W4237378708"],"related_works":["https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W2084813257","https://openalex.org/W2045929470","https://openalex.org/W2081127504","https://openalex.org/W2122223946","https://openalex.org/W4233500668","https://openalex.org/W1974145978","https://openalex.org/W1977867163","https://openalex.org/W2393426762"],"abstract_inverted_index":{"BACKGROUND:":[0],"TNF":[1,51,146],"(Tumor":[2],"Necrosis":[3],"Factor-\u03b1)":[4],"induces":[5],"HUVEC":[6,53],"(Human":[7],"Umbilical":[8],"Vein":[9],"Endothelial":[10],"Cells)":[11],"to":[12,60,74,102,134,165,182,260,268],"proliferate":[13],"and":[14,28,119,169,201,205,218,249],"form":[15],"new":[16],"blood":[17],"vessels.":[18],"This":[19,252],"TNF-induced":[20,37,66,126,191,207,213,244],"angiogenesis":[21,38,135,214,245],"plays":[22],"a":[23,55,116,197,232,265],"key":[24],"role":[25,241],"in":[26,52,82,177,242,247],"cancer":[27,248],"rheumatic":[29,250],"disease.":[30,251,272],"However,":[31],"the":[32,45,62,83,109,145,189,243],"molecular":[33,63,234],"system":[34,64,235],"that":[35,100,196,236,255],"underlies":[36],"is":[39],"largely":[40],"unknown.":[41],"METHODS:":[42],"We":[43],"analyzed":[44],"gene":[46,78,112,127,151,192,228],"expression":[47,79,152],"changes":[48],"stimulated":[49,147],"by":[50,136,155,215],"over":[54],"time":[56,84,148],"course":[57,85,149],"using":[58,90,115],"microarrays":[59],"reveal":[61],"underlying":[65],"angiogenesis.":[67,170,208],"Traditional":[68],"k-means":[69,142],"clustering":[70,143],"analysis":[71,89,114,158,230,253,258],"was":[72,92],"performed":[73,94],"identify":[75],"informative":[76,103,162],"temporal":[77],"patterns":[80],"buried":[81],"data.":[86],"Functional":[87],"enrichment":[88,157],"DAVID":[91],"then":[93,106],"for":[95,111,131],"each":[96],"cluster.":[97],"The":[98],"genes":[99,176],"belonged":[101],"clusters":[104,163,173],"were":[105,180],"used":[107,181],"as":[108],"input":[110],"network":[113,118,229,257],"Bayesian":[117,185,256],"nonparametric":[120],"regression":[121],"method.":[122],"Based":[123,187],"on":[124,188],"this":[125],"network,":[128],"we":[129,194],"searched":[130],"sub-networks":[132],"related":[133,164],"integrating":[137],"existing":[138],"biological":[139],"knowledge.":[140],"RESULTS:":[141],"of":[144],"microarray":[150],"data,":[153],"followed":[154],"functional":[156,261],"identified":[159],"three":[160,172],"biologically":[161],"apoptosis,":[166],"cellular":[167],"proliferation":[168],"These":[171],"included":[174],"648":[175],"total,":[178],"which":[179,220],"estimate":[183],"dynamic":[184],"networks.":[186],"estimated":[190],"networks,":[193],"hypothesized":[195],"sub-network":[198],"including":[199],"IL6":[200,211],"IL8":[202],"inhibits":[203],"apoptosis":[204],"promotes":[206,212],"More":[209],"particularly,":[210],"inducing":[216],"NF-\u03baB":[217],"IL8,":[219],"are":[221],"strong":[222],"cell":[223],"growth":[224],"factors.":[225],"CONCLUSIONS:":[226],"Computational":[227],"revealed":[231],"novel":[233],"may":[237,263],"play":[238],"an":[239],"important":[240],"seen":[246],"suggests":[254],"linked":[259],"annotation":[262],"be":[264],"powerful":[266],"tool":[267],"provide":[269],"insight":[270],"into":[271]},"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":2}],"updated_date":"2026-08-23T07:36:19.812096","created_date":"2025-10-10T00:00:00"}