{"id":"https://openalex.org/W3021664743","doi":"https://doi.org/10.1093/bib/bbaa081","title":"Reference genome and annotation updates lead to contradictory prognostic predictions in gene expression signatures: a case study of resected stage I lung adenocarcinoma","display_name":"Reference genome and annotation updates lead to contradictory prognostic predictions in gene expression signatures: a case study of resected stage I lung adenocarcinoma","publication_year":2020,"publication_date":"2020-05-05","ids":{"openalex":"https://openalex.org/W3021664743","doi":"https://doi.org/10.1093/bib/bbaa081","mag":"3021664743","pmid":"https://pubmed.ncbi.nlm.nih.gov/32383445"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa081","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa081","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5089862145","display_name":"Zheyang Zhang","orcid":"https://orcid.org/0009-0006-3923-6864"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zheyang Zhang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083495525","display_name":"Sainan Zhang","orcid":"https://orcid.org/0000-0001-7258-4592"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sainan Zhang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100353939","display_name":"Xin Li","orcid":"https://orcid.org/0000-0002-7414-5734"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xin Li","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025129892","display_name":"Zhangxiang Zhao","orcid":"https://orcid.org/0000-0001-7467-7223"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhangxiang Zhao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016774012","display_name":"Changjing Chen","orcid":"https://orcid.org/0000-0003-3679-0131"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Changjing Chen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051903143","display_name":"Juxuan Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Juxuan Zhang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103048922","display_name":"Mengyue Li","orcid":"https://orcid.org/0009-0007-4798-5651"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mengyue Li","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059703535","display_name":"Zixin Wei","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zixin Wei","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003849963","display_name":"Wenbin Jiang","orcid":"https://orcid.org/0009-0004-8559-2734"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wenbin Jiang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102008964","display_name":"Bo Pan","orcid":"https://orcid.org/0000-0002-8448-6268"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bo Pan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100414389","display_name":"Ying Li","orcid":"https://orcid.org/0000-0003-0863-4967"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ying Li","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100386691","display_name":"Yixin Liu","orcid":"https://orcid.org/0000-0003-4401-9291"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yixin Liu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061549769","display_name":"Yingyue Cao","orcid":"https://orcid.org/0000-0003-3218-1160"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yingyue Cao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043417955","display_name":"Wenyuan Zhao","orcid":"https://orcid.org/0000-0002-6477-9434"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wenyuan Zhao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069723993","display_name":"Yunyan Gu","orcid":"https://orcid.org/0000-0001-5693-4126"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yunyan Gu","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-5693-4126","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003421192","display_name":"Yan Yu","orcid":"https://orcid.org/0000-0001-7177-7552"},"institutions":[{"id":"https://openalex.org/I156144747","display_name":"Harbin Medical University","ror":"https://ror.org/05jscf583","country_code":"CN","type":"education","lineage":["https://openalex.org/I156144747"]},{"id":"https://openalex.org/I4210103956","display_name":"Third Affiliated Hospital of Harbin Medical University","ror":"https://ror.org/01f77gp95","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210103956"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yan Yu","raw_affiliation_strings":["Yan Yu, Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yan Yu, Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China","institution_ids":["https://openalex.org/I156144747","https://openalex.org/I4210103956"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004766617","display_name":"Qingwei Meng","orcid":null},"institutions":[{"id":"https://openalex.org/I156144747","display_name":"Harbin Medical University","ror":"https://ror.org/05jscf583","country_code":"CN","type":"education","lineage":["https://openalex.org/I156144747"]},{"id":"https://openalex.org/I4210103956","display_name":"Third Affiliated Hospital of Harbin Medical University","ror":"https://ror.org/01f77gp95","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210103956"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qingwei Meng","raw_affiliation_strings":["Qingwei Meng, Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Qingwei Meng, Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin 150040, China","institution_ids":["https://openalex.org/I156144747","https://openalex.org/I4210103956"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032948942","display_name":"Lishuang Qi","orcid":"https://orcid.org/0000-0002-2991-6544"},"institutions":[{"id":"https://openalex.org/I156144747","display_name":"Harbin Medical University","ror":"https://ror.org/05jscf583","country_code":"CN","type":"education","lineage":["https://openalex.org/I156144747"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lishuang Qi","raw_affiliation_strings":["Corresponding authors: Lishuang Qi, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China. Tel.: +86-451-8661-5933"],"raw_orcid":"https://orcid.org/0000-0002-2991-6544","affiliations":[{"raw_affiliation_string":"Corresponding authors: Lishuang Qi, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China. Tel.: +86-451-8661-5933","institution_ids":["https://openalex.org/I156144747"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5003421192","https://openalex.org/A5004766617","https://openalex.org/A5032948942"],"corresponding_institution_ids":["https://openalex.org/I156144747","https://openalex.org/I4210103956"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.4779,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.56122742,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"22","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11482","display_name":"RNA modifications and cancer","score":0.9986000061035156,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/annotation","display_name":"Annotation","score":0.6554122567176819},{"id":"https://openalex.org/keywords/stage","display_name":"Stage (stratigraphy)","score":0.6259531378746033},{"id":"https://openalex.org/keywords/adenocarcinoma","display_name":"Adenocarcinoma","score":0.6140381097793579},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5600738525390625},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5116241574287415},{"id":"https://openalex.org/keywords/lung","display_name":"Lung","score":0.4247726798057556},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41732925176620483},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40009361505508423},{"id":"https://openalex.org/keywords/oncology","display_name":"Oncology","score":0.3248492181301117},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3100489377975464},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.30591580271720886},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.2918698191642761},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.23458555340766907},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23421910405158997}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6554122567176819},{"id":"https://openalex.org/C146357865","wikidata":"https://www.wikidata.org/wiki/Q1123245","display_name":"Stage (stratigraphy)","level":2,"score":0.6259531378746033},{"id":"https://openalex.org/C2781182431","wikidata":"https://www.wikidata.org/wiki/Q356033","display_name":"Adenocarcinoma","level":3,"score":0.6140381097793579},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5600738525390625},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5116241574287415},{"id":"https://openalex.org/C2777714996","wikidata":"https://www.wikidata.org/wiki/Q7886","display_name":"Lung","level":2,"score":0.4247726798057556},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41732925176620483},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40009361505508423},{"id":"https://openalex.org/C143998085","wikidata":"https://www.wikidata.org/wiki/Q162555","display_name":"Oncology","level":1,"score":0.3248492181301117},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3100489377975464},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.30591580271720886},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.2918698191642761},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.23458555340766907},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23421910405158997},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000601","qualifier_name":"surgery","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000601","qualifier_name":"surgery","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000601","qualifier_name":"surgery","is_major_topic":false},{"descriptor_ui":"D005557","descriptor_name":"Formaldehyde","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005557","descriptor_name":"Formaldehyde","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005557","descriptor_name":"Formaldehyde","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":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000601","qualifier_name":"surgery","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000601","qualifier_name":"surgery","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000601","qualifier_name":"surgery","is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016612","descriptor_name":"Paraffin Embedding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016612","descriptor_name":"Paraffin Embedding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016612","descriptor_name":"Paraffin Embedding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016707","descriptor_name":"Tissue Fixation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016707","descriptor_name":"Tissue Fixation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016707","descriptor_name":"Tissue Fixation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053208","descriptor_name":"Kaplan-Meier Estimate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053208","descriptor_name":"Kaplan-Meier Estimate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053208","descriptor_name":"Kaplan-Meier Estimate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa081","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa081","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32383445","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32383445","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.7200000286102295,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G335574062","display_name":null,"funder_award_id":"81672931","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4655669100","display_name":"\u57fa\u4e8e\u57fa\u56e0\u95f4\u9057\u4f20\u4e92\u4f5c\u89e3\u6790\u764c\u75c7\u9776\u5411\u836f\u7269\u8010\u836f\u673a\u5236","funder_award_id":"61673143","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5127079047","display_name":null,"funder_award_id":"81872396","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8354568183","display_name":"\u80bf\u7624\u6cbb\u7597\u65b9\u6848\u591a\u51b3\u7b56\u8282\u70b9\u7684\u4e2a\u4f53\u5316\u591a\u7ea7\u9884\u540e\u9884\u6d4b\u6807\u5fd7\u8bc6\u522b\u7b56\u7565","funder_award_id":"61701143","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":49,"referenced_works":["https://openalex.org/W1893007615","https://openalex.org/W1968239355","https://openalex.org/W1983083208","https://openalex.org/W1986077582","https://openalex.org/W2009965783","https://openalex.org/W2016848076","https://openalex.org/W2026635277","https://openalex.org/W2031330193","https://openalex.org/W2042690128","https://openalex.org/W2062346641","https://openalex.org/W2096192437","https://openalex.org/W2104549677","https://openalex.org/W2107903949","https://openalex.org/W2107986563","https://openalex.org/W2110065044","https://openalex.org/W2113620105","https://openalex.org/W2115157373","https://openalex.org/W2123664981","https://openalex.org/W2129925362","https://openalex.org/W2130116522","https://openalex.org/W2131478115","https://openalex.org/W2137096454","https://openalex.org/W2138207763","https://openalex.org/W2140405760","https://openalex.org/W2154431984","https://openalex.org/W2170989872","https://openalex.org/W2171528238","https://openalex.org/W2171981087","https://openalex.org/W2179438025","https://openalex.org/W2247766769","https://openalex.org/W2542677082","https://openalex.org/W2564732085","https://openalex.org/W2580314844","https://openalex.org/W2588167481","https://openalex.org/W2591928747","https://openalex.org/W2733991343","https://openalex.org/W2756432050","https://openalex.org/W2787788280","https://openalex.org/W2884930815","https://openalex.org/W2896246551","https://openalex.org/W2898598946","https://openalex.org/W2901214479","https://openalex.org/W2912573440","https://openalex.org/W2947780575","https://openalex.org/W2950929224","https://openalex.org/W2978549968","https://openalex.org/W2992931937","https://openalex.org/W4237403594","https://openalex.org/W4245204182"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2251519152"],"abstract_inverted_index":{"RNA-sequencing":[0,139],"enables":[1],"accurate":[2],"and":[3,14,43,57,84,94,118,183,197],"low-cost":[4],"transcriptome-wide":[5],"detection.":[6],"However,":[7],"expression":[8],"estimates":[9],"vary":[10],"as":[11],"reference":[12,55,181],"genomes":[13,56],"gene":[15,92],"annotations":[16,90],"are":[17],"updated,":[18],"confounding":[19],"existing":[20,176],"expression-based":[21],"prognostic":[22,25,79,109,177,195],"signatures.":[23],"Herein,":[24],"9-gene":[26],"pair":[27],"signature":[28],"(GPS)":[29],"was":[30,135],"applied":[31],"to":[32,180,193],"197":[33],"patients":[34,63],"with":[35,53,142,160],"stage":[36,126,157],"I":[37,127,158],"lung":[38],"adenocarcinoma":[39],"derived":[40],"from":[41,46],"previous":[42],"latest":[44],"data":[45,123,140],"The":[47],"Cancer":[48],"Genome":[49],"Atlas":[50],"(TCGA)":[51],"processed":[52,141],"different":[54],"annotations.":[58],"For":[59],"9-GPS,":[60],"6.6%":[61],"of":[62,100,124,175],"exhibited":[64],"discordant":[65,102],"risk":[66,103],"classifications":[67],"between":[68],"the":[69,97,143,173],"two":[70],"TCGA":[71],"versions.":[72],"Similar":[73],"results":[74],"were":[75,96],"observed":[76],"for":[77,91,155],"other":[78],"signatures,":[80],"including":[81],"IRGPI,":[82],"15-gene":[83],"ORACLE.":[85],"We":[86],"found":[87],"that":[88],"conflicting":[89],"length":[93],"overlap":[95],"major":[98],"cause":[99],"their":[101],"classification.":[104],"Therefore,":[105],"we":[106],"constructed":[107],"a":[108],"40-GPS":[110,151,186],"based":[111],"on":[112],"stable":[113,137],"genes":[114],"across":[115],"GENCODE":[116,145,148],"v20-v30":[117],"validated":[119],"it":[120],"using":[121],"public":[122],"471":[125],"samples":[128,159],"(log-rank":[129,164],"P":[130,165],"<":[131],"0.0010).":[132],"Risk":[133],"classification":[134,198],"still":[136],"in":[138],"newest":[144],"v32":[146],"versus":[147],"v20-v30.":[149],"Specifically,":[150],"could":[152],"predict":[153],"survival":[154],"30":[156],"formalin-fixed":[161],"paraffin-embedded":[162],"tissues":[163],"=":[166],"0.0177).":[167],"In":[168],"conclusion,":[169],"this":[170],"method":[171],"overcomes":[172],"vulnerability":[174],"signatures":[178],"due":[179,192],"genome":[182],"annotation":[184],"updates.":[185],"may":[187],"offer":[188],"individualized":[189],"clinical":[190],"applications":[191],"its":[194],"accuracy":[196],"stability.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
