{"id":"https://openalex.org/W2117179247","doi":"https://doi.org/10.1093/bioinformatics/btv265","title":"PAGER: constructing PAGs and new PAG\u2013PAG relationships for network biology","display_name":"PAGER: constructing PAGs and new PAG\u2013PAG relationships for network biology","publication_year":2015,"publication_date":"2015-06-10","ids":{"openalex":"https://openalex.org/W2117179247","doi":"https://doi.org/10.1093/bioinformatics/btv265","mag":"2117179247","pmid":"https://pubmed.ncbi.nlm.nih.gov/26072489"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv265","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv265","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i250/17103058/btv265.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i250/17103058/btv265.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041167576","display_name":"Zongliang Yue","orcid":"https://orcid.org/0000-0001-8290-123X"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Zongliang Yue","raw_affiliation_strings":["1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China"],"affiliations":[{"raw_affiliation_string":"1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China","institution_ids":["https://openalex.org/I27781120","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112231554","display_name":"Madhura M. Kshirsagar","orcid":null},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Madhura M. Kshirsagar","raw_affiliation_strings":["1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China"],"affiliations":[{"raw_affiliation_string":"1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China","institution_ids":["https://openalex.org/I27781120","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086559814","display_name":"Thanh Nguyen","orcid":"https://orcid.org/0000-0002-8440-1594"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Thanh Nguyen","raw_affiliation_strings":["1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China"],"affiliations":[{"raw_affiliation_string":"1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China","institution_ids":["https://openalex.org/I27781120","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001546652","display_name":"Chayaporn Suphavilai","orcid":"https://orcid.org/0000-0002-4777-4586"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Chayaporn Suphavilai","raw_affiliation_strings":["1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China"],"affiliations":[{"raw_affiliation_string":"1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China","institution_ids":["https://openalex.org/I27781120","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033034306","display_name":"Michael T. Neylon","orcid":"https://orcid.org/0000-0001-6868-6852"},"institutions":[{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Michael T. Neylon","raw_affiliation_strings":["1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China"],"affiliations":[{"raw_affiliation_string":"1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China","institution_ids":["https://openalex.org/I27781120","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102148356","display_name":"Liugen Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Liugen Zhu","raw_affiliation_strings":["1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China"],"affiliations":[{"raw_affiliation_string":"1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China","institution_ids":["https://openalex.org/I27781120","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081030515","display_name":"Timothy L. Ratliff","orcid":"https://orcid.org/0000-0003-4221-5416"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]},{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Timothy Ratliff","raw_affiliation_strings":["1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China"],"affiliations":[{"raw_affiliation_string":"1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China","institution_ids":["https://openalex.org/I27781120","https://openalex.org/I55769427"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058469124","display_name":"Jake Y. Chen","orcid":"https://orcid.org/0000-0001-8829-7504"},"institutions":[{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jake Y. Chen","raw_affiliation_strings":["1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China"],"affiliations":[{"raw_affiliation_string":"1 Indiana University School of Informatics and Computing, 2Department of Computer and Information Science, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, 3Purdue University Center for Cancer Research, West Lafayette, IN 47906 and 4Institute of Biopharmaceutical Informatics and Technology, Wenzhou Medical University, WenZhou, Zhe Jiang Province, China","institution_ids":["https://openalex.org/I27781120","https://openalex.org/I55769427"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5041167576"],"corresponding_institution_ids":["https://openalex.org/I27781120","https://openalex.org/I55769427"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.9038,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.74578856,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"31","issue":"12","first_page":"i250","last_page":"i257"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.996399998664856,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9902999997138977,"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/pager","display_name":"Pager","score":0.9469804763793945},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5232207775115967},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41932493448257446},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.37860536575317383},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.36292600631713867},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.21045920252799988},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1768425703048706}],"concepts":[{"id":"https://openalex.org/C127611570","wikidata":"https://www.wikidata.org/wiki/Q832436","display_name":"Pager","level":2,"score":0.9469804763793945},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5232207775115967},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41932493448257446},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37860536575317383},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36292600631713867},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.21045920252799988},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1768425703048706}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","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:10.1093/bioinformatics/btv265","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv265","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i250/17103058/btv265.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26072489","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26072489","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:3535716","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4553834","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/12/i250","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/12/i250","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"},{"id":"pmh:oai:scholarworks.indianapolis.iu.edu:1805/8860","is_oa":false,"landing_page_url":"https://hdl.handle.net/1805/8860","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PMC","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv265","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv265","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/12/i250/17103058/btv265.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310263","display_name":"Indiana University-Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2117179247.pdf","grobid_xml":"https://content.openalex.org/works/W2117179247.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W72712630","https://openalex.org/W1589164005","https://openalex.org/W1969808215","https://openalex.org/W1974385622","https://openalex.org/W1974436271","https://openalex.org/W1984581368","https://openalex.org/W1987979808","https://openalex.org/W1988393300","https://openalex.org/W2010457001","https://openalex.org/W2010502047","https://openalex.org/W2028133290","https://openalex.org/W2041953582","https://openalex.org/W2048296798","https://openalex.org/W2048384644","https://openalex.org/W2052250375","https://openalex.org/W2057545775","https://openalex.org/W2060880575","https://openalex.org/W2066351138","https://openalex.org/W2096766502","https://openalex.org/W2097789418","https://openalex.org/W2100899895","https://openalex.org/W2100980426","https://openalex.org/W2103017472","https://openalex.org/W2108539496","https://openalex.org/W2111573647","https://openalex.org/W2114830914","https://openalex.org/W2116868464","https://openalex.org/W2122683221","https://openalex.org/W2124388496","https://openalex.org/W2127745238","https://openalex.org/W2130410032","https://openalex.org/W2130666470","https://openalex.org/W2133465414","https://openalex.org/W2133998111","https://openalex.org/W2134316325","https://openalex.org/W2135329546","https://openalex.org/W2138906045","https://openalex.org/W2141703917","https://openalex.org/W2143017117","https://openalex.org/W2154947819","https://openalex.org/W2155330008","https://openalex.org/W2157269800","https://openalex.org/W2157795344","https://openalex.org/W2159482845","https://openalex.org/W2165040702","https://openalex.org/W2167540852","https://openalex.org/W2169622100","https://openalex.org/W2171322586","https://openalex.org/W2312949642","https://openalex.org/W2412058973","https://openalex.org/W2605068739","https://openalex.org/W4212920271","https://openalex.org/W4236802399","https://openalex.org/W4237360036","https://openalex.org/W4242404314","https://openalex.org/W4294107304","https://openalex.org/W6715395527"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2018407952","https://openalex.org/W2470754505","https://openalex.org/W1124711469","https://openalex.org/W2154411704","https://openalex.org/W2379913586","https://openalex.org/W2197984350","https://openalex.org/W3125776761","https://openalex.org/W2053727034","https://openalex.org/W2028231728"],"abstract_inverted_index":{"In":[0,18],"this":[1,19],"article,":[2],"we":[3,21,100],"described":[4],"a":[5,33,52,102,172],"new":[6],"database":[7,42,59,128,198],"framework":[8],"to":[9,132,135,149,181],"perform":[10],"integrative":[11,184],"\"gene-set,":[12],"network,":[13],"and":[14,29,48,77,88,118,137,192],"pathway":[15],"analysis\"":[16],"(GNPA).":[17],"framework,":[20],"integrated":[22],"heterogeneous":[23],"data":[24,179,190],"on":[25],"pathways,":[26],"annotated":[27],"list,":[28],"gene-sets":[30],"(PAGs)":[31],"into":[32,45],"PAG":[34],"electronic":[35],"repository":[36],"(PAGER).":[37],"PAGs":[38,50,117,120,139],"in":[39,161],"the":[40],"PAGER":[41,58,127,145,197],"are":[43],"organized":[44],"P-type,":[46],"A-type":[47],"G-type":[49],"with":[51,121],"three-letter-code":[53],"standard":[54],"naming":[55],"convention.":[56],"The":[57,196],"currently":[60],"compiles":[61],"44":[62],"313":[63],"genes":[64],"from":[65,140],"5":[66],"species":[67],"including":[68],"human,":[69],"38":[70],"663":[71],"PAGs,":[72],"324":[73],"830":[74],"gene-gene":[75],"relationships":[76],"two":[78],"types":[79],"of":[80,112,125],"3":[81],"174":[82],"323":[83],"PAG-PAG":[84,151],"regulatory":[85,89,152],"relationships-co-membership":[86],"based":[87],"relationship":[90],"based.":[91],"To":[92],"help":[93,133,186],"users":[94,134,148],"assess":[95],"each":[96],"PAG's":[97],"biological":[98,157,194],"relevance,":[99],"developed":[101],"cohesion":[103],"measure":[104],"called":[105],"Cohesion":[106],"Coefficient":[107],"(CoCo),":[108],"which":[109],"is":[110],"capable":[111],"disambiguating":[113],"between":[114],"biologically":[115],"significant":[116],"random":[119],"an":[122],"area-under-curve":[123],"performance":[124],"0.98.":[126],"was":[129],"set":[130,163],"up":[131],"search":[136],"retrieve":[138],"its":[141],"online":[142],"web":[143],"interface.":[144],"enable":[146],"advanced":[147],"build":[150],"networks":[153],"that":[154],"provide":[155,171],"complementary":[156],"insights":[158],"not":[159],"found":[160],"gene":[162,167],"analysis":[164],"or":[165],"individual":[166],"network":[168,188],"analysis.":[169],"We":[170],"case":[173],"study":[174],"using":[175],"cancer":[176],"functional":[177],"genomics":[178],"sets":[180],"demonstrate":[182],"how":[183],"GNPA":[185],"improve":[187],"biology":[189],"coverage":[191],"therefore":[193],"interpretability.":[195],"can":[199],"be":[200],"accessible":[201],"openly":[202],"at":[203],"http://discovery.informatics.iupui.edu/PAGER/.":[204]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-03-26T15:22:09.906841","created_date":"2025-10-10T00:00:00"}
