{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T19:52:02Z","timestamp":1774468322500,"version":"3.50.1"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,3,28]],"date-time":"2024-03-28T00:00:00Z","timestamp":1711584000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"publisher","award":["82173645"],"award-info":[{"award-number":["82173645"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Nature Science Foundation of China","doi-asserted-by":"publisher","award":["82341109"],"award-info":[{"award-number":["82341109"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2022FZZX03-03-07"],"award-info":[{"award-number":["2022FZZX03-03-07"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Enrichment analysis contextualizes biological features in pathways to facilitate a systematic understanding of high-dimensional data and is widely used in biomedical research. The emerging reporter score-based analysis (RSA) method shows more promising sensitivity, as it relies on P-values instead of raw values of features. However, RSA cannot be directly applied to multi-group and longitudinal experimental designs and is often misused due to the lack of a proper tool. Here, we propose the Generalized Reporter Score-based Analysis (GRSA) method for multi-group and longitudinal omics data. A comparison with other popular enrichment analysis methods demonstrated that GRSA had increased sensitivity across multiple benchmark datasets. We applied GRSA to microbiome, transcriptome and metabolome data and discovered new biological insights in omics studies. Finally, we demonstrated the application of GRSA beyond functional enrichment using a taxonomy database. We implemented GRSA in an R package, ReporterScore, integrating with a powerful visualization module and updatable pathway databases, which is available on the Comprehensive R Archive Network (https:\/\/cran.r-project.org\/web\/packages\/ReporterScore). We believe that the ReporterScore package will be a valuable asset for broad biomedical research fields.<\/jats:p>","DOI":"10.1093\/bib\/bbae116","type":"journal-article","created":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T09:09:01Z","timestamp":1709284141000},"source":"Crossref","is-referenced-by-count":50,"title":["Generalized reporter score-based enrichment analysis for omics data"],"prefix":"10.1093","volume":"25","author":[{"given":"Chen","family":"Peng","sequence":"first","affiliation":[{"name":"MOE Key Laboratory of Biosystems Homeostasis & Protection , and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, , Hangzhou, Zhejiang 310030 , China"},{"name":"Life Sciences Institute, Zhejiang University , and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, , Hangzhou, Zhejiang 310030 , China"},{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases , First Affiliated Hospital, , Hangzhou, Zhejiang 310009 , China"},{"name":"Zhejiang University School of Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang 310009 , China"}]},{"given":"Qiong","family":"Chen","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Biosystems Homeostasis & Protection , and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, , Hangzhou, Zhejiang 310030 , China"},{"name":"Life Sciences Institute, Zhejiang University , and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, , Hangzhou, Zhejiang 310030 , China"},{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases , First Affiliated Hospital, , Hangzhou, Zhejiang 310009 , China"},{"name":"Zhejiang University School of Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang 310009 , China"}]},{"given":"Shangjin","family":"Tan","sequence":"additional","affiliation":[{"name":"BGI Research , Wuhan, Hubei 430074 , China"},{"name":"BGI Research , Shenzhen, Guangdong 518083 , China"}]},{"given":"Xiaotao","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Genetics, Stanford University School of Medicine , Stanford, CA , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0260-7271","authenticated-orcid":false,"given":"Chao","family":"Jiang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Biosystems Homeostasis & Protection , and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, , Hangzhou, Zhejiang 310030 , China"},{"name":"Life Sciences Institute, Zhejiang University , and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, , Hangzhou, Zhejiang 310030 , China"},{"name":"State Key Laboratory for Diagnosis and Treatment of Infectious Diseases , First Affiliated Hospital, , Hangzhou, Zhejiang 310009 , China"},{"name":"Zhejiang University School of Medicine , First Affiliated Hospital, , Hangzhou, Zhejiang 310009 , China"},{"name":"Center for Life Sciences, Shaoxing Institute, Zhejiang University , Shaoxing, Zhejiang 321000 , China"}]}],"member":"286","published-online":{"date-parts":[[2024,3,27]]},"reference":[{"key":"2024032812415459800_ref1","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1016\/j.tig.2023.01.003","article-title":"Interpreting omics data with pathway enrichment analysis","volume":"39","author":"Zhao","year":"2023","journal-title":"Trends Genet"},{"key":"2024032812415459800_ref2","doi-asserted-by":"crossref","first-page":"bbac143","DOI":"10.1093\/bib\/bbac143","article-title":"On the influence of several factors on pathway enrichment analysis","volume":"23","author":"Mubeen","year":"2022","journal-title":"Brief Bioinform"},{"key":"2024032812415459800_ref3","doi-asserted-by":"crossref","first-page":"W216","DOI":"10.1093\/nar\/gkac194","article-title":"DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)","volume":"50","author":"Sherman","year":"2022","journal-title":"Nucleic 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