{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T11:11:24Z","timestamp":1763809884628,"version":"3.37.3"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2018,7,13]],"date-time":"2018-07-13T00:00:00Z","timestamp":1531440000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["21477087","91643201"],"award-info":[{"award-number":["21477087","91643201"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Minister of Science and Technology of China","award":["2016YFC0206507"],"award-info":[{"award-number":["2016YFC0206507"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"NIDDK","doi-asserted-by":"publisher","award":["R01DK106593","U24DK062429"],"award-info":[{"award-number":["R01DK106593","U24DK062429"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000066","name":"NIEHS","doi-asserted-by":"publisher","award":["1R01ES029212-01"],"award-info":[{"award-number":["1R01ES029212-01"]}],"id":[{"id":"10.13039\/100000066","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Summary level data of GWAS becomes increasingly important in post-GWAS data mining. Here, we present GIGSEA (Genotype Imputed Gene Set Enrichment Analysis), a novel method that uses GWAS summary statistics and eQTL to infer differential gene expression and interrogate gene set enrichment for the trait-associated SNPs. By incorporating empirical eQTL of the disease relevant tissue, GIGSEA naturally accounts for factors such as gene size, gene boundary, SNP distal regulation and multiple-marker regulation. The weighted linear regression model was used to perform the enrichment test, properly adjusting for imputation accuracy, model incompleteness and redundancy in different gene sets. The significance level of enrichment is assessed by the permutation test, where matrix operation was employed to dramatically improve computation speed. GIGSEA has appropriate type I error rates, and discovers the plausible biological findings on the real data set.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>GIGSEA is implemented in R, and freely available at www.github.com\/zhushijia\/GIGSEA.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty529","type":"journal-article","created":{"date-parts":[[2018,7,13]],"date-time":"2018-07-13T11:20:55Z","timestamp":1531480855000},"page":"160-163","source":"Crossref","is-referenced-by-count":14,"title":["GIGSEA: genotype imputed gene set enrichment analysis using GWAS summary level data"],"prefix":"10.1093","volume":"35","author":[{"given":"Shijia","family":"Zhu","sequence":"first","affiliation":[{"name":"Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA"}]},{"given":"Tongqi","family":"Qian","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA"}]},{"given":"Yujin","family":"Hoshida","sequence":"additional","affiliation":[{"name":"Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, Division of Digestive and Liver Diseases, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA"}]},{"given":"Yuan","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China"}]},{"given":"Jing","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China"}]},{"given":"Ke","family":"Hao","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA"},{"name":"Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China"}]}],"member":"286","published-online":{"date-parts":[[2018,7,13]]},"reference":[{"key":"2023013107201740500_bty529-B1","article-title":"Integrating tissue specific mechanisms into GWAS summary results","volume":"045260","author":"Barbeira","year":"2016","journal-title":"bioRxiv"},{"key":"2023013107201740500_bty529-B2","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1101\/gr.155192.113","article-title":"Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals","volume":"24","author":"Battle","year":"2014","journal-title":"Genome Res"},{"key":"2023013107201740500_bty529-B3","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1038\/nature13595","article-title":"Biological insights from 108 schizophrenia-associated genetic loci","volume":"511","author":"Consortium,SWGotPG","year":"2014","journal-title":"Nature"},{"key":"2023013107201740500_bty529-B4","doi-asserted-by":"crossref","first-page":"e1004219","DOI":"10.1371\/journal.pcbi.1004219","article-title":"MAGMA: generalized gene-set analysis of GWAS data","volume":"11","author":"de Leeuw","year":"2015","journal-title":"PLoS Comput. 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