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The model also incorporates the functional annotation of known genes to guide the clustering procedure.<\/jats:p><jats:p>Results: We applied our model to the clustering of 79 chemogenomic experiments in yeast. Known pleiotropic genes PDR5 and MAL11 are more accurately represented by the model than by a clustering procedure that requires genes to belong to a single cluster. Drugs such as miconazole and fenpropimorph that have different targets but similar off-target genes are clustered more accurately by the model-based framework. We show that this model is useful for summarizing the relationship among treatments and genes affected by those treatments in a compendium of microarray profiles.<\/jats:p><jats:p>Availability: Supplementary information and computer code at http:\/\/genomics.lbl.gov\/llda<\/jats:p><jats:p>Contact: \u00a0flaherty@berkeley.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti515","type":"journal-article","created":{"date-parts":[[2005,5,27]],"date-time":"2005-05-27T00:24:34Z","timestamp":1117153474000},"page":"3286-3293","source":"Crossref","is-referenced-by-count":50,"title":["A latent variable model for chemogenomic profiling"],"prefix":"10.1093","volume":"21","author":[{"given":"Patrick","family":"Flaherty","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guri","family":"Giaever","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jochen","family":"Kumm","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael I.","family":"Jordan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adam P.","family":"Arkin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2005,5,26]]},"reference":[{"key":"2023051612004086300_B1","doi-asserted-by":"crossref","unstructured":"Alexandersson, M., et al. 2003SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. 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