OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments.
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.


CONCLUSIONS
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.
Price
Morgan N
MN
Lawrence Berkeley Lab, Mailstop 977-152, Berkeley, CA 94720, USA. morgannprice@yahoo.com
Arkin
Adam P
AP
Alm
Eric J
EJ
D000465:Algorithms; D001426:Bacterial Proteins / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D009876:Operon / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012984:Software
D001426:Bacterial Proteins