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To integrate information among multiple studies at the pathway level, pathway\u2010based meta\u2010analysis can be performed. Paired or partially paired samples are common in biomedical research. However, there are currently no existing pathway\u2010based meta\u2010analysis methods appropriate for paired or partially paired study designs.<\/jats:p><jats:p>In this study, we developed a pathway\u2010based meta\u2010analysis approach for paired or partially paired samples. Meta\u2010analysis on the transcriptomics profiles were conducted using p\u2010value\u2010based, rank\u2010based, and effect size\u2010based algorithms. The application of our approach was demonstrated using partially paired data from psoriasis transcriptomics studies.<\/jats:p><jats:p>Upon combining six transcriptomics studies, genes related to the cell cycle and DNA replication pathways are found to be highly perturbed in psoriatic lesional skin samples. Results were validated externally with independent RNA\u2010Seq data. Comparison with existing pathway meta\u2010analysis methods revealed consistent results, with our method showing higher detection power.<\/jats:p><jats:p>This study demonstrated the utility of our newly developed pathway\u2010based meta\u2010analysis that allows the incorporation of partially paired or paired samples. The proposed framework can be applied to omics data including but not limited to transcriptomics data.<\/jats:p>","DOI":"10.1002\/jrsm.1381","type":"journal-article","created":{"date-parts":[[2019,11,4]],"date-time":"2019-11-04T13:19:11Z","timestamp":1572873551000},"page":"123-133","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Pathway\u2010based meta\u2010analysis for partially paired transcriptomics analysis"],"prefix":"10.1002","volume":"11","author":[{"given":"Wing Tung","family":"Fung","sequence":"first","affiliation":[{"name":"School of Public Health, Li Ka Shing Faculty of Medicine The University of Hong Kong Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph T.","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Public Health, Li Ka Shing Faculty of Medicine The University of Hong Kong Hong Kong, 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