{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T04:30:47Z","timestamp":1787977847849,"version":"build-2784847793"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006899","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,4,12]],"date-time":"2019-04-12T00:00:00Z","timestamp":1555027200000}}],"reference-count":26,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2019,4,2]],"date-time":"2019-04-02T00:00:00Z","timestamp":1554163200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U19AI117873"],"award-info":[{"award-number":["U19AI117873"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"United States-Isreal Binational Science Foundation","award":["2013395"],"award-info":[{"award-number":["2013395"]}]},{"DOI":"10.13039\/501100001742","name":"United States-Israel Binational Science Foundation","doi-asserted-by":"publisher","award":["2013395"],"award-info":[{"award-number":["2013395"]}],"id":[{"id":"10.13039\/501100001742","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006899","type":"journal-article","created":{"date-parts":[[2019,4,2]],"date-time":"2019-04-02T13:38:32Z","timestamp":1554212312000},"page":"e1006899","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":23,"title":["Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE)"],"prefix":"10.1371","volume":"15","author":[{"given":"Hailong","family":"Meng","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9311-9884","authenticated-orcid":true,"given":"Gur","family":"Yaari","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher R.","family":"Bolen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Avey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4957-1544","authenticated-orcid":true,"given":"Steven H.","family":"Kleinstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,4,2]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1186\/1471-2407-8-394","article-title":"Gene expression meta-analysis identifies metastatic pathways and transcription factors in breast cancer","volume":"8","author":"M Thomassen","year":"2008","journal-title":"BMC cancer"},{"issue":"D1","key":"ref2","doi-asserted-by":"crossref","first-page":"D457","DOI":"10.1093\/nar\/gkv1070","article-title":"KEGG as a reference resource for gene and protein annotation","volume":"44","author":"M Kanehisa","year":"2016","journal-title":"Nucleic acids research"},{"issue":"D1","key":"ref3","doi-asserted-by":"crossref","first-page":"D472","DOI":"10.1093\/nar\/gkt1102","article-title":"The Reactome pathway knowledgebase","volume":"42","author":"D Croft","year":"2014","journal-title":"Nucleic acids research"},{"issue":"2","key":"ref4","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/ni.2789","article-title":"Molecular signatures of antibody responses derived from a systems biology study of five human vaccines","volume":"15","author":"S Li","year":"2014","journal-title":"Nature immunology"},{"issue":"12","key":"ref5","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"A Liberzon","year":"2011","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"43","key":"ref6","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"A Subramanian","year":"2005","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"9","key":"ref7","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1093\/bioinformatics\/bti260","article-title":"Significance analysis of functional categories in gene expression studies: a structured permutation approach","volume":"21","author":"WT Barry","year":"2005","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"W Huang da","year":"2009","journal-title":"Nature protocols"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/1471-2105-10-47","article-title":"A general modular framework for gene set enrichment analysis","volume":"10","author":"M Ackermann","year":"2009","journal-title":"BMC bioinformatics"},{"issue":"8","key":"ref10","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1093\/bioinformatics\/btm051","article-title":"Analyzing gene expression data in terms of gene sets: methodological issues","volume":"23","author":"JJ Goeman","year":"2007","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"1","key":"ref11","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gkw797","article-title":"Methods to increase reproducibility in differential gene expression via meta-analysis","volume":"45","author":"TE Sweeney","year":"2017","journal-title":"Nucleic acids research"},{"issue":"1","key":"ref12","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1093\/nar\/30.1.207","article-title":"Gene Expression Omnibus: NCBI gene expression and hybridization array data repository","volume":"30","author":"R Edgar","year":"2002","journal-title":"Nucleic acids research"},{"issue":"10","key":"ref13","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1093\/bioinformatics\/btq148","article-title":"Meta-analysis for pathway enrichment analysis when combining multiple genomic studies","volume":"26","author":"K Shen","year":"2010","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"7","key":"ref14","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1093\/bioinformatics\/btt068","article-title":"A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies","volume":"29","author":"M Chen","year":"2013","journal-title":"Bioinformatics (Oxford, England)"},{"issue":"4","key":"ref15","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1002\/sim.7540","article-title":"Meta-analysis approaches to combine multiple gene set enrichment studies","volume":"37","author":"W Lu","year":"2018","journal-title":"Statistics in medicine"},{"issue":"18","key":"ref16","doi-asserted-by":"crossref","first-page":"e170","DOI":"10.1093\/nar\/gkt660","article-title":"Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations","volume":"41","author":"G Yaari","year":"2013","journal-title":"Nucleic acids research"},{"issue":"2","key":"ref17","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/nmeth.3252","article-title":"Orchestrating high-throughput genomic analysis with Bioconductor","volume":"12","author":"W Huber","year":"2015","journal-title":"Nature methods"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1186\/s12859-015-0707-9","article-title":"Quantitative gene set analysis generalized for repeated measures, confounder adjustment, and continuous covariates","volume":"16","author":"JA Turner","year":"2015","journal-title":"BMC bioinformatics"},{"issue":"14","key":"ref19","article-title":"Multicohort analysis reveals baseline transcriptional predictors of influenza vaccination responses","volume":"2","year":"2017","journal-title":"Science immunology"},{"issue":"17","key":"ref20","doi-asserted-by":"crossref","first-page":"e134","DOI":"10.1093\/nar\/gks457","article-title":"Quantifying selection in high-throughput Immunoglobulin sequencing data sets","volume":"40","author":"G Yaari","year":"2012","journal-title":"Nucleic acids research"},{"issue":"1","key":"ref21","doi-asserted-by":"crossref","first-page":"38","DOI":"10.18632\/aging.100720","article-title":"Aging-dependent alterations in gene expression and a mitochondrial signature of responsiveness to human influenza vaccination","volume":"7","author":"J Thakar","year":"2015","journal-title":"Aging"},{"issue":"2","key":"ref22","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.cell.2014.03.031","article-title":"Global analyses of human immune variation reveal baseline predictors of postvaccination responses","volume":"157","author":"JS Tsang","year":"2014","journal-title":"Cell"},{"issue":"5","key":"ref23","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1080\/00031305.1948.10483405","article-title":"Questions and answers #14","volume":"2","author":"F Mosteller","year":"1948","journal-title":"The American Statistician"},{"key":"ref24","article-title":"The American Soldier","volume":"1","author":"S Stouffer","year":"1949"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v036.i03","article-title":"Conducting Meta-Analyses in R with the metafor Package","volume":"36","author":"W Viechtbauer","year":"2010","journal-title":"J Stat Softw"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1214\/10-AOAS393","article-title":"An adaptively weighted statistic for detecting differential gene expression when combining multiple transcriptomic studies","volume":"5","author":"Ja Li","year":"2011","journal-title":"The Annals of Applied Statistics"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006899","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,4,12]],"date-time":"2019-04-12T00:00:00Z","timestamp":1555027200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006899","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,16]],"date-time":"2024-07-16T10:45:57Z","timestamp":1721126757000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006899"}},"subtitle":[],"editor":[{"given":"Mihaela","family":"Pertea","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,4,2]]},"references-count":26,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2019,4,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006899","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1006899","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,2]]}}}