Transcriptograms: A Genome-Wide Gene Expression Analysis Method

In this chapter, we discuss the Transcriptogram method for statistically analyzing differential gene expression in a genome-wide profile. This technique suggests a method to hierarchically interrogate the data and, subsequently, narrow down to gene level. We present the method, discuss its reproducibility and enhanced signal-to-noise ratio, and discuss its application in investigating time series data as in cell cycle, therapy gene target identification, lineage and tissue classification and as a powerful test to identify error and assess the quality of normalization procedures. We finally present the software ready for download and discuss the R-plugin for BioConductor.