{"id":"https://openalex.org/W7125811520","doi":"https://doi.org/10.1021/acs.jcim.5c02241","title":"PharmGEO: A Curated Atlas of Drug-Response Transcriptomes Enabling Cross-Study Comparisons","display_name":"PharmGEO: A Curated Atlas of Drug-Response Transcriptomes Enabling Cross-Study Comparisons","publication_year":2026,"publication_date":"2026-01-27","ids":{"openalex":"https://openalex.org/W7125811520","doi":"https://doi.org/10.1021/acs.jcim.5c02241","pmid":"https://pubmed.ncbi.nlm.nih.gov/41589333"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02241","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02241","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5123918375","display_name":"Haoran Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210112069","display_name":"Theranostics (New Zealand)","ror":"https://ror.org/02wykja76","country_code":"NZ","type":"company","lineage":["https://openalex.org/I4210112069"]},{"id":"https://openalex.org/I83519826","display_name":"Nanjing Medical University","ror":"https://ror.org/059gcgy73","country_code":"CN","type":"education","lineage":["https://openalex.org/I83519826"]}],"countries":["CN","NZ"],"is_corresponding":false,"raw_author_name":"Haoran Chen","raw_affiliation_strings":["Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics","Nanjing Medical University"],"raw_orcid":"https://orcid.org/0000-0002-1666-3226","affiliations":[{"raw_affiliation_string":"Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics","institution_ids":["https://openalex.org/I4210112069"]},{"raw_affiliation_string":"Nanjing Medical University","institution_ids":["https://openalex.org/I83519826"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123962794","display_name":"Mujin Li","orcid":null},"institutions":[{"id":"https://openalex.org/I130828816","display_name":"University of Leeds","ror":"https://ror.org/024mrxd33","country_code":"GB","type":"education","lineage":["https://openalex.org/I130828816"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mujin Li","raw_affiliation_strings":["University of Leeds"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Leeds","institution_ids":["https://openalex.org/I130828816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124038567","display_name":"Jie Geng","orcid":null},"institutions":[{"id":"https://openalex.org/I2802939634","display_name":"Chinese PLA General Hospital","ror":"https://ror.org/04gw3ra78","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802939634"]},{"id":"https://openalex.org/I4210126592","display_name":"National Clinical Research","ror":"https://ror.org/03ddkvp86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210126592"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jie Geng","raw_affiliation_strings":["Department of Hematology, National Clinical Research Center for Geriatric Disease","The Second Medical Center of Chinese PLA General Hospital"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Hematology, National Clinical Research Center for Geriatric Disease","institution_ids":["https://openalex.org/I4210126592"]},{"raw_affiliation_string":"The Second Medical Center of Chinese PLA General Hospital","institution_ids":["https://openalex.org/I2802939634"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124020578","display_name":"Chen Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I4210112069","display_name":"Theranostics (New Zealand)","ror":"https://ror.org/02wykja76","country_code":"NZ","type":"company","lineage":["https://openalex.org/I4210112069"]},{"id":"https://openalex.org/I83519826","display_name":"Nanjing Medical University","ror":"https://ror.org/059gcgy73","country_code":"CN","type":"education","lineage":["https://openalex.org/I83519826"]}],"countries":["CN","NZ"],"is_corresponding":true,"raw_author_name":"Chen Cao","raw_affiliation_strings":["Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics","Nanjing Medical University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics","institution_ids":["https://openalex.org/I4210112069"]},{"raw_affiliation_string":"Nanjing Medical University","institution_ids":["https://openalex.org/I83519826"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5123907369","display_name":"Jianxin Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I17747738","display_name":"Beijing University of Chinese Medicine","ror":"https://ror.org/05damtm70","country_code":"CN","type":"education","lineage":["https://openalex.org/I17747738"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianxin Chen","raw_affiliation_strings":["Beijing University of Chinese Medicine","School of Traditional Chinese Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing University of Chinese Medicine","institution_ids":["https://openalex.org/I17747738"]},{"raw_affiliation_string":"School of Traditional Chinese Medicine","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5123907369","https://openalex.org/A5124020578"],"corresponding_institution_ids":["https://openalex.org/I17747738","https://openalex.org/I4210112069","https://openalex.org/I83519826"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10965377,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"66","issue":"3","first_page":"1301","last_page":"1308"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.595300018787384,"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":0.595300018787384,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.29899999499320984,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.025599999353289604,"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/metadata","display_name":"Metadata","score":0.7950000166893005},{"id":"https://openalex.org/keywords/atlas","display_name":"Atlas (anatomy)","score":0.7534000277519226},{"id":"https://openalex.org/keywords/repurposing","display_name":"Repurposing","score":0.6974999904632568},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.6951000094413757},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5746999979019165},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.4607999920845032},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4569000005722046},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.43860000371932983},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.40549999475479126}],"concepts":[{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.7950000166893005},{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.7534000277519226},{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.6974999904632568},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.6951000094413757},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6083999872207642},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5746999979019165},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5392000079154968},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.4607999920845032},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4569000005722046},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.43860000371932983},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.40549999475479126},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.38580000400543213},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37369999289512634},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.35749998688697815},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3564999997615814},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3179999887943268},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.3109000027179718},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2964000105857849},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2953999936580658},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2777999937534332},{"id":"https://openalex.org/C55282118","wikidata":"https://www.wikidata.org/wiki/Q252683","display_name":"Snapshot (computer storage)","level":2,"score":0.27639999985694885},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.27059999108314514},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.26750001311302185},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.26649999618530273},{"id":"https://openalex.org/C64903051","wikidata":"https://www.wikidata.org/wiki/Q2198549","display_name":"Drug development","level":3,"score":0.26570001244544983},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.26460000872612},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2630999982357025},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.26159998774528503},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.26089999079704285}],"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c02241","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02241","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:41589333","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41589333","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5798893398","display_name":null,"funder_award_id":"62231013","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5906459449","display_name":null,"funder_award_id":"62471240","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W2001318056","https://openalex.org/W2045949302","https://openalex.org/W2057685090","https://openalex.org/W2130410032","https://openalex.org/W2146512944","https://openalex.org/W2179438025","https://openalex.org/W2249991663","https://openalex.org/W2302501749","https://openalex.org/W2553758616","https://openalex.org/W2612467560","https://openalex.org/W2949216109","https://openalex.org/W2953067954","https://openalex.org/W2991579922","https://openalex.org/W3021575042","https://openalex.org/W3105014258","https://openalex.org/W3119203274","https://openalex.org/W3155253210","https://openalex.org/W3175752499","https://openalex.org/W3180093102","https://openalex.org/W3206046197","https://openalex.org/W4254687493","https://openalex.org/W4280489006","https://openalex.org/W4296039169","https://openalex.org/W4321374315","https://openalex.org/W4323036511","https://openalex.org/W4367312557","https://openalex.org/W4387599780","https://openalex.org/W4388454971","https://openalex.org/W4388615774","https://openalex.org/W4388615780","https://openalex.org/W4402135271","https://openalex.org/W4403334384","https://openalex.org/W4403479107","https://openalex.org/W4403479110","https://openalex.org/W4403859766","https://openalex.org/W4411929908"],"related_works":[],"abstract_inverted_index":{"Drug-induced":[0],"transcriptomic":[1,122],"profiles":[2],"capture":[3],"how":[4,133],"compounds":[5],"reprogram":[6],"genes":[7,90],"and":[8,12,17,36,41,48,60,72,98,109,129,138],"pathways":[9],"across":[10,65],"dose":[11],"time,":[13,35],"supporting":[14],"drug-gene":[15,103],"associations":[16,104],"interaction":[18,115,139],"analysis.":[19],"The":[20],"field":[21],"faces":[22],"a":[23,79,86,111,146],"practical":[24],"bottleneck:":[25],"GEO":[26],"drug":[27,136,151],"studies":[28,125,144],"are":[29,39,70,76],"scattered,":[30],"metadata":[31],"for":[32],"dose,":[33],"exposure":[34],"cell":[37],"type":[38],"inconsistent,":[40],"processing":[42],"pipelines":[43],"differ,":[44],"which":[45],"limits":[46],"reuse":[47],"fair":[49],"comparison.":[50],"We":[51],"built":[52],"PharmGEO,":[53],"an":[54],"interactive":[55,95],"Shiny":[56],"resource":[57],"that":[58],"curates":[59],"standardizes":[61],"7,931":[62],"pharmaco-transcriptomic":[63],"experiments":[64],"1,334":[66],"drugs.":[67],"Key":[68],"variables":[69],"harmonized,":[71],"all":[73],"data":[74],"sets":[75],"reprocessed":[77],"through":[78],"single":[80],"pipeline,":[81],"yielding":[82],"transcriptome-wide":[83],"results":[84],"with":[85,117],"mean":[87],"of":[88,150],"17,776":[89],"per":[91],"experiment.":[92],"PharmGEO":[93,134,153],"supports":[94],"differential":[96],"expression":[97],"pathway":[99],"enrichment,":[100],"prioritizes":[101],"high-confidence":[102],"using":[105],"cross-data":[106],"set":[107],"consistency,":[108],"provides":[110],"directionally":[112],"annotated":[113],"drug-drug":[114],"network":[116],"115,264":[118],"interactions":[119],"derived":[120],"from":[121],"overlap.":[123],"Case":[124],"in":[126],"target":[127],"validation":[128],"combination":[130],"assessment":[131],"show":[132],"enables":[135],"repurposing":[137],"evaluation":[140],"by":[141],"turning":[142],"heterogeneous":[143],"into":[145],"coherent,":[147],"searchable":[148],"atlas":[149],"responses.":[152],"is":[154],"available":[155],"at":[156],"http://www.pharmgeo.net.":[157]},"counts_by_year":[],"updated_date":"2026-06-04T09:04:59.091469","created_date":"2026-01-28T00:00:00"}