{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,6]],"date-time":"2024-06-06T22:36:35Z","timestamp":1717713395245},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: It is important to consider finding differentially expressed genes in a dataset of microarray experiments for pattern generation.<\/jats:p>\n               <jats:p>Results: We developed two methods which are mainly based on the q-values approach; the first is a direct extension of the q-values approach, while the second uses two approaches: q-values and maximum-likelihood. We present two algorithms for the second method, one for error minimization and the other for confidence bounding. Also, we show how the method called Patterns from Gene Expression (PaGE) (Grant et al., 2000) can benefit from q-values. Finally, we conducted some experiments to demonstrate the effectiveness of the proposed methods; experimental results on a selected dataset (BRCA1 vs BRCA2 tumor types) are provided.<\/jats:p>\n               <jats:p>Contact: \u00a0alhajj@cpsc.ucalgary.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti189","type":"journal-article","created":{"date-parts":[[2004,12,18]],"date-time":"2004-12-18T01:16:41Z","timestamp":1103332601000},"page":"445-450","source":"Crossref","is-referenced-by-count":5,"title":["Finding differentially expressed genes for pattern generation"],"prefix":"10.1093","volume":"21","author":[{"given":"Osman","family":"Abul","sequence":"first","affiliation":[]},{"given":"Reda","family":"Alhajj","sequence":"additional","affiliation":[]},{"given":"Faruk","family":"Polat","sequence":"additional","affiliation":[]},{"given":"Ken","family":"Barker","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,12,17]]},"reference":[{"key":"2023013107235386700_B1","unstructured":"Claverie, J.M. 1999Computational methods for the identification of differential and coordinated gene expression. Hum. Mol. Genet.81821\u20131832"},{"key":"2023013107235386700_B2","doi-asserted-by":"crossref","unstructured":"Manduchi, E., Grant, G.R., McKenzie, S.E., Overton, G.C., Surrey, S., Stoeckert, C.J., Jr. 2000Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. Bioinformatics16685\u2013698","DOI":"10.1093\/bioinformatics\/16.8.685"},{"key":"2023013107235386700_B3","unstructured":"Technical Report No. 578. Dudoit, S., Yang, Y.H., Speed, T.P., Callow, M.J. 2002Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments.  , Berkeley, CA  University of California"},{"key":"2023013107235386700_B4","unstructured":"Technical Report No. 633. Ge, Y., Dudoit, S., Speed, P.S. 2003Statistical methods for identifying-differentially expressed genes in replicated cDNA microarray experiment.  , Berkeley, CA  University of California"},{"key":"2023013107235386700_B5","unstructured":"Storey, J.D. 2002False discovery rates: theory and applications to DNA microarrays.  , CA  PhD Thesis Department of Statistics, Stanford University"},{"key":"2023013107235386700_B6","unstructured":"Hedenfalk, I., Duggan, D., Chen, Y., Radmacher, M., Bittner, M., Simon, R., Meltzer, P., Gusterson, B., Esteller, M., Kallioniemi, O.P., et al. 2001Gene-expression profiles in hereditary breast Cancer. N. Engl. J. Med.344539\u2013548"},{"key":"2023013107235386700_B7","unstructured":"Grant, G.R., Manduchi, E., Stoeckert, C.J. 2000Using non-parametric methods in the context of multiple testing to identify differentially expressed genes. Proceedings of Critical Assessment of Techniques for Microarray Data Analysis (CAMDA'00) , Durham, NC  December 18\u201319 Duke University"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/4\/445\/48965155\/bioinformatics_21_4_445.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/4\/445\/48965155\/bioinformatics_21_4_445.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T09:56:43Z","timestamp":1675159003000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/4\/445\/203583"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,12,17]]},"references-count":7,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2005,2,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti189","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,2,15]]},"published":{"date-parts":[[2004,12,17]]}}}