Identifying differential expression in multiple SAGE libraries: an overdispersed log-linear model approach

In this article, we introduce an overdispersed log-linear model approach to analyzing SAGE; we evaluate and compare its performance with three other tests: the two-sample t test, tw test and another based on overdispersed logistic linear regression. Analysis of simulated and real datasets show that both the log-linear and logistic overdispersion methods generally perform better than the t and tw tests; the log-linear method is further found to have better performance than the logistic method, showing equal or higher statistical power over a range of parameter values and with different data distributions.Overdispersed log-linear models provide an attractive and reliable framework for analyzing SAGE experiments involving multiple libraries. For convenience, the implementation of this method is available through a user-friendly web-interface available at http://www.cbcb.duke.edu/sage webcite.Serial analysis of gene expression (SAGE) is used to measure relative abundances of messenger RNAs (mRNAs) for a large number of genes [1,2]. Briefly, mRNAs are extracted from biological samples and reverse-transcribed to cDNAs. The double-stranded cDNAs are then digested by a 4-cutter restriction enzyme (anchoring enzymes, usually NlaIII). After digestion, another restriction enzyme (tagging enzymes) is used to release the downstream DNA sequences at 3' of most of the anchoring enzyme restriction sites. The released sequences, usually 10–11 base pairs (bp) long, are called SAGE tags. The tags derived from many different species of mRNAs can be concatenated, cloned and sequenced. In a typical SAGE experiment, a large number of tags (often ranging from 30,000 to 100,000) are collected from each sample, with each tag representing, ideally, one gene; the tag count indicates the transcription level of the gene represented by that specific tag. A natural question of interest is whether a given tag is differentially expressed. Over the past few years, SAGE has been extensively used for e