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Brilliant specifically incorporates genome and\/or phenotype grouping structures, as well as phenotype correlation structures, in feature selection, effect estimation, and outcome prediction under a penalized multi-response linear regression model. Extensive simulations demonstrate its superior performance compared to competing methods. We applied Brilliant to two omics studies. In the first study, we identified novel association signals between multivariate gene expressions and high-dimensional DNA methylation profiles, providing biological insights for the baseline CpG-to-gene regulation patterns in a Puerto Rican children asthma cohort. The second study focused on cell-type deconvolution prediction using high-dimensional gene expression profiles. Using Brilliant, we improved the accuracy for cell-type fraction prediction and identified novel cell-type signature genes.<\/jats:p>","DOI":"10.1093\/bib\/bbae585","type":"journal-article","created":{"date-parts":[[2024,10,30]],"date-time":"2024-10-30T16:19:41Z","timestamp":1730305181000},"source":"Crossref","is-referenced-by-count":1,"title":["Molecular group and correlation guided structural learning for multi-phenotype prediction"],"prefix":"10.1093","volume":"25","author":[{"given":"Xueping","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Biostatistics, University of Pittsburgh , Pittsburgh, PA 15216 ,","place":["United States"]}]},{"given":"Manqi","family":"Cai","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Pittsburgh , Pittsburgh, PA 15216 ,","place":["United States"]}]},{"given":"Molin","family":"Yue","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Pittsburgh , Pittsburgh, PA 15216 ,","place":["United States"]}]},{"given":"Juan C","family":"Celed\u00f3n","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Pittsburgh Medical Center Children\u2019s Hospital of Pittsburgh , Pittsburgh, PA 15224 ,","place":["United States"]}]},{"given":"Jiebiao","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Pittsburgh , Pittsburgh, PA 15216 ,","place":["United States"]}]},{"given":"Ying","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Pittsburgh , Pittsburgh, PA 15216 ,","place":["United States"]}]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of Pittsburgh Medical Center Children\u2019s Hospital of Pittsburgh , Pittsburgh, PA 15224 ,","place":["United States"]}]},{"given":"Yanming","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics & Data Science, University of Kansas Medical Center , Kansas, KS 66160 ,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2024,11,14]]},"reference":[{"key":"2024111416091303600_ref1","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1080\/10618600.2012.681250","article-title":"A sparse-group lasso","volume":"22","author":"Simon","year":"2013","journal-title":"J Comput Graph Stat"},{"key":"2024111416091303600_ref2","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1111\/j.1467-9868.2005.00532.x","article-title":"Model selection and estimation in regression with grouped variables","volume":"68","author":"Yuan","year":"2006","journal-title":"J R Stat Soc Series B Stat Methodol"},{"key":"2024111416091303600_ref3","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1111\/j.2517-6161.1996.tb02080.x","article-title":"Regression shrinkage and selection via the lasso","volume":"58","author":"Tibshirani","year":"1996","journal-title":"J R Stat Soc B Methodol"},{"key":"2024111416091303600_ref4","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1111\/j.1467-9868.2005.00503.x","article-title":"Regularization and variable selection via the elastic net","volume":"67","author":"Zou","year":"2005","journal-title":"J R Stat Soc Series B Stat Methodol"},{"key":"2024111416091303600_ref5","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1111\/biom.12292","article-title":"Multivariate sparse group lasso for the multivariate multiple linear regression with an arbitrary group structure","volume":"71","author":"Li","year":"2015","journal-title":"Biometrics"},{"key":"2024111416091303600_ref6","doi-asserted-by":"publisher","first-page":"668","DOI":"10.1080\/02664763.2017.1289503","article-title":"An algorithm for the multivariate group lasso with covariance estimation","volume":"45","author":"Wilms","year":"2018","journal-title":"J Appl Stat"},{"key":"2024111416091303600_ref7","doi-asserted-by":"publisher","first-page":"432","DOI":"10.1093\/biostatistics\/kxm045","article-title":"Sparse inverse covariance estimation with the graphical lasso","volume":"9","author":"Friedman","year":"2008","journal-title":"Biostatistics"},{"key":"2024111416091303600_ref8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v033.i01","article-title":"Regularization paths for generalized linear models via coordinate descent","volume":"33","author":"Friedman","year":"2010","journal-title":"J Stat Softw"},{"key":"2024111416091303600_ref9","first-page":"336","article-title":"Dna methylation in nasal epithelium, atopy, and atopic asthma in children: a genome-wide study. 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