{"id":"https://openalex.org/W2111573647","doi":"https://doi.org/10.1186/1471-2105-13-s15-s2","title":"PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries","display_name":"PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries","publication_year":2012,"publication_date":"2012-09-01","ids":{"openalex":"https://openalex.org/W2111573647","doi":"https://doi.org/10.1186/1471-2105-13-s15-s2","mag":"2111573647","pmid":"https://pubmed.ncbi.nlm.nih.gov/23046413"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s15-s2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s15-s2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S15-S2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S15-S2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100609552","display_name":"Hui Huang","orcid":"https://orcid.org/0000-0001-7305-5860"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hui Huang","raw_affiliation_strings":["School of Informatics, Indiana University, Indianapolis, IN 46202, USA","School of Informatics, Indiana University, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045121596","display_name":"Xiaogang Wu","orcid":"https://orcid.org/0000-0003-4373-6926"},"institutions":[{"id":"https://openalex.org/I2802576979","display_name":"Indianapolis Zoo","ror":"https://ror.org/01k9v9b21","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802576979"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"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":["US"],"is_corresponding":false,"raw_author_name":"Xiaogang Wu","raw_affiliation_strings":["Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA","MedeoLinx, LLC, Indianapolis, IN 46280, USA","School of Informatics, Indiana University, Indianapolis, IN 46202, USA","School of Informatics, Indiana University, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"MedeoLinx, LLC, Indianapolis, IN 46280, USA","institution_ids":["https://openalex.org/I2802576979"]},{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050019853","display_name":"Madhankumar Sonachalam","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"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":["US"],"is_corresponding":false,"raw_author_name":"Madhankumar Sonachalam","raw_affiliation_strings":["Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA","Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049581157","display_name":"Sammed N. Mandape","orcid":"https://orcid.org/0000-0002-3984-4150"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sammed N Mandape","raw_affiliation_strings":["School of Informatics, Indiana University, Indianapolis, IN 46202, USA","School of Informatics, Indiana University, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071816838","display_name":"Ragini Pandey","orcid":null},"institutions":[{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"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":["US"],"is_corresponding":false,"raw_author_name":"Ragini Pandey","raw_affiliation_strings":["Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA","Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032987775","display_name":"Karl F. MacDorman","orcid":"https://orcid.org/0000-0003-1093-4184"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karl F MacDorman","raw_affiliation_strings":["School of Informatics, Indiana University, Indianapolis, IN 46202, USA","School of Informatics, Indiana University, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101932818","display_name":"Ping Wan","orcid":"https://orcid.org/0000-0003-1552-0124"},"institutions":[{"id":"https://openalex.org/I96852419","display_name":"Capital Normal University","ror":"https://ror.org/005edt527","country_code":"CN","type":"education","lineage":["https://openalex.org/I96852419"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ping Wan","raw_affiliation_strings":["Capital Normal University, Beijing, 100048, China","Capital Normal University, Beijing, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Capital Normal University, Beijing, 100048, China","institution_ids":["https://openalex.org/I96852419"]},{"raw_affiliation_string":"Capital Normal University, Beijing, China","institution_ids":["https://openalex.org/I96852419"]}]},{"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/I2802576979","display_name":"Indianapolis Zoo","ror":"https://ror.org/01k9v9b21","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802576979"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"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":["US"],"is_corresponding":true,"raw_author_name":"Jake Y Chen","raw_affiliation_strings":["Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA","MedeoLinx, LLC, Indianapolis, IN 46280, USA","School of Informatics, Indiana University, Indianapolis, IN 46202, USA","School of Informatics, Indiana University, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana Center for Systems Biology and Personalized Medicine, Indiana University, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I55769427"]},{"raw_affiliation_string":"MedeoLinx, LLC, Indianapolis, IN 46280, USA","institution_ids":["https://openalex.org/I2802576979"]},{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, IN 46202, USA","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"School of Informatics, Indiana University, Indianapolis, USA","institution_ids":["https://openalex.org/I55769427"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5058469124","https://openalex.org/A5101932818"],"corresponding_institution_ids":["https://openalex.org/I2802576979","https://openalex.org/I4210155419","https://openalex.org/I55769427","https://openalex.org/I96852419"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.35,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.79837604,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"13","issue":"S15","first_page":"S2","last_page":"S2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8942000269889832,"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":0.8942000269889832,"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":0.022099999710917473,"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"}},{"id":"https://openalex.org/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.014999999664723873,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.6061998009681702},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5415371656417847},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5397006869316101},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4893497824668884},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4778542220592499},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.4573885500431061},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4460596740245819},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4239954948425293},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.410614550113678},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.21500834822654724},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13724854588508606}],"concepts":[{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.6061998009681702},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5415371656417847},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5397006869316101},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4893497824668884},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4778542220592499},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.4573885500431061},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4460596740245819},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4239954948425293},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.410614550113678},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.21500834822654724},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13724854588508606}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"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":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-13-s15-s2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s15-s2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S15-S2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23046413","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23046413","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 bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:dbc93e6dfeb749349f2f8fa2c5dcbf6c","is_oa":false,"landing_page_url":"https://doaj.org/article/dbc93e6dfeb749349f2f8fa2c5dcbf6c","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 Bioinformatics, Vol 13, Iss Suppl 15, p S2 (2012)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3439733","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3439733","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 Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s15-s2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s15-s2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S15-S2","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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 Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309036","display_name":"Purdue University","ror":"https://ror.org/02dqehb95"},{"id":"https://openalex.org/F4320310263","display_name":"Indiana University-Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08"},{"id":"https://openalex.org/F4320333591","display_name":"Multidisciplinary University Research Initiative","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2111573647.pdf","grobid_xml":"https://content.openalex.org/works/W2111573647.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1565377632","https://openalex.org/W1751728186","https://openalex.org/W1965256295","https://openalex.org/W1967418905","https://openalex.org/W2010457001","https://openalex.org/W2012280706","https://openalex.org/W2020541351","https://openalex.org/W2023929969","https://openalex.org/W2048296798","https://openalex.org/W2072573412","https://openalex.org/W2072664252","https://openalex.org/W2084974619","https://openalex.org/W2100899895","https://openalex.org/W2100980426","https://openalex.org/W2119412782","https://openalex.org/W2122630333","https://openalex.org/W2123836768","https://openalex.org/W2130410032","https://openalex.org/W2134118500","https://openalex.org/W2138906045","https://openalex.org/W2154437541","https://openalex.org/W2155142785","https://openalex.org/W2169622100","https://openalex.org/W2184417913","https://openalex.org/W2953965357"],"related_works":["https://openalex.org/W1840542775","https://openalex.org/W2416830231","https://openalex.org/W179926425","https://openalex.org/W2003932708","https://openalex.org/W3003578468","https://openalex.org/W2336657400","https://openalex.org/W2284877871","https://openalex.org/W2086883243","https://openalex.org/W2088351705","https://openalex.org/W2551532359"],"abstract_inverted_index":{"BACKGROUND:":[0],"Over":[1],"the":[2,13,54,71,103,120,154,160],"past":[3],"decade,":[4],"pathway":[5,25,32,219],"and":[6,23,33,89,107,144,196],"gene-set":[7,34,168],"enrichment":[8,35,231],"analysis":[9,36,177,220],"has":[10],"evolved":[11],"into":[12],"study":[14],"of":[15,57,125,136,156,162],"high-throughput":[16],"functional":[17,204],"genomics.":[18,205],"Owing":[19],"to":[20,30,43,78,185,190,201],"poorly":[21],"annotated":[22],"incomplete":[24],"data,":[26],"researchers":[27],"have":[28,65],"begun":[29],"combine":[31],"as":[37,39,97,167,178],"well":[38],"network":[40,90,198],"module-based":[41],"approaches":[42,221],"identify":[44],"crucial":[45,192],"relationships":[46,163],"between":[47,164],"different":[48],"molecular":[49,58,98,225],"mechanisms.":[50],"METHODS:":[51],"To":[52],"meet":[53],"new":[55],"challenge":[56],"phenotype":[59],"discovery,":[60],"in":[61,159],"this":[62,187],"work,":[63],"we":[64,113,182],"developed":[66],"an":[67],"integrated":[68,208],"online":[69,111,209],"database,":[70],"Pathway":[72],"And":[73],"Gene":[74],"Enrichment":[75],"Database":[76],"(PAGED),":[77],"enable":[79],"comprehensive":[80,122],"searches":[81],"for":[82,214,223,228],"disease-specific":[83],"pathways,":[84,193],"gene":[85,126,138,165,194,197],"signatures,":[86,195],"microRNA":[87],"targets,":[88],"modules":[91,199],"by":[92,118],"integrating":[93],"gene-set-based":[94],"prior":[95],"knowledge":[96],"patterns":[99],"from":[100,147],"multiple":[101],"levels:":[102],"genome,":[104],"transcriptome,":[105],"post-transcriptome,":[106],"proteome.":[108],"RESULTS:":[109],"The":[110],"database":[112,188,210],"developed,":[114],"PAGED":[115,132,157],"http://bio.informatics.iupui.edu/PAGED":[116],"is":[117],"far":[119],"most":[121],"public":[123],"compilation":[124],"sets.":[127],"In":[128],"its":[129,152],"current":[130],"release,":[131],"contains":[133],"a":[134,179,212],"total":[135],"25,242":[137],"sets,":[139],"61,413":[140],"genes,":[141],"20":[142],"organisms,":[143],"1,275,560":[145],"records":[146],"five":[148],"major":[149],"categories.":[150],"Beyond":[151],"size,":[153],"advantage":[155],"lies":[158],"explorations":[161],"sets":[166],"association":[169],"networks":[170],"(GSANs).":[171],"Using":[172],"colorectal":[173,202],"cancer":[174,203],"expression":[175],"data":[176],"case":[180],"study,":[181],"demonstrate":[183],"how":[184],"query":[186],"resource":[189],"discover":[191],"specific":[200],"CONCLUSIONS:":[206],"This":[207],"lays":[211],"foundation":[213],"developing":[215],"tools":[216],"beyond":[217],"third-generation":[218],"on":[222],"discovering":[224],"phenotypes,":[226],"especially":[227],"disease-associated":[229],"pathway/gene-set":[230],"analysis.":[232]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
