Software
OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments
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* Corresponding author: Eric J Alm ejalm@mit.edu
1 Lawrence Berkeley Lab, 1 Cyclotron Road, Mailstop 977-152, Berkeley CA 94720, USA
2 Virtual Institute of Microbial Stress and Survival
3 Howard Hughes Medical Institute, Berkeley CA, USA
4 University of California at Berkeley, Department of Bioengineering, Berkeley CA, USA
BMC Bioinformatics 2006, 7:19 doi:10.1186/1471-2105-7-19
Published: 13 January 2006Abstract
Background
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.
Conclusion
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 webcite.