OpWise: Operons aid the identification of differentially expressedgenes in bacterial microarray experiments

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Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. Results-OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based ... continued below

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Price, Morgan N.; Arkin, Adam P. & Alm, Eric J. November 23, 2005.

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Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known. Results-OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon. Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available at http://microbesonline.org/OpWise.

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  • Journal Name: BioMed Bioinformatics; Journal Volume: 7; Journal Issue: 19; Related Information: Journal Publication Date: 13 January2006

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  • Report No.: LBNL--59159
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 889893
  • Archival Resource Key: ark:/67531/metadc884555

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  • November 23, 2005

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  • Sept. 21, 2016, 2:29 a.m.

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  • Sept. 30, 2016, 12:37 p.m.

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Price, Morgan N.; Arkin, Adam P. & Alm, Eric J. OpWise: Operons aid the identification of differentially expressedgenes in bacterial microarray experiments, article, November 23, 2005; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc884555/: accessed September 22, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.