{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,7]],"date-time":"2026-02-07T15:38:11Z","timestamp":1770478691848,"version":"3.49.0"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Identification of transcription factor binding motifs (TFBMs) is a crucial first step towards the understanding of regulatory circuitries controlling the expression of genes. In this paper, we propose a novel procedure called regularized sliced inverse regression (RSIR) for identifying TFBMs. RSIR follows a recent trend to combine information contained in both gene expression measurements and genes' promoter sequences. Compared with existing methods, RSIR is efficient in computation, very stable for data with high dimensionality and high collinearity, and improves motif detection sensitivities and specificities by avoiding inappropriate model specification.<\/jats:p>\n               <jats:p>Results: We compare RSIR with SIR and stepwise regression based on simulated data and find that RSIR has a lower false positive rate. We also demonstrate an excellent performance of RSIR by applying it to the yeast amino acid starvation data and cell cycle data.<\/jats:p>\n               <jats:p>Availability: Matlab programs are available upon request from the authors.<\/jats:p>\n               <jats:p>Contact: \u00a0jliu@stat.harvard.edu; yuzhu@stat.purdue.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti680","type":"journal-article","created":{"date-parts":[[2005,9,16]],"date-time":"2005-09-16T00:12:50Z","timestamp":1126829570000},"page":"4169-4175","source":"Crossref","is-referenced-by-count":54,"title":["RSIR: regularized sliced inverse regression for motif discovery"],"prefix":"10.1093","volume":"21","author":[{"given":"Wenxuan","family":"Zhong","sequence":"first","affiliation":[{"name":"Department of Statistics, Harvard University 1 \u00a0 1 \u00a0 \u00a0 Cambridge, MA 02138, USA"}]},{"given":"Peng","family":"Zeng","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, Auburn University 2 \u00a0 2 \u00a0 \u00a0 Auburn, AL 36849, USA"}]},{"given":"Ping","family":"Ma","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Illinois at Urbana-Champaign 3 \u00a0 3 \u00a0 \u00a0 Champaign, IL 61820, USA"}]},{"given":"Jun S.","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Statistics, Harvard University 1 \u00a0 1 \u00a0 \u00a0 Cambridge, MA 02138, USA"}]},{"given":"Yu","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Statistics, Purdue University 4 \u00a0 4 \u00a0 \u00a0 West Lafayette, IN 47907, USA"}]}],"member":"286","published-online":{"date-parts":[[2005,9,15]]},"reference":[{"key":"2023061007105293900_b1","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/S0092-8674(04)00304-6","article-title":"Predicting gene expression from sequence","volume":"117","author":"Beer","year":"2004","journal-title":"Cell"},{"key":"2023061007105293900_b2","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/84792","article-title":"Regulatory element detection using correlation with expression","volume":"27","author":"Bussemaker","year":"2001","journal-title":"Nat. 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