Our approach thus ensures comparability to previously published in vitro data (including previous microarray data, for example [ 26, 36- 38]).
We cannot completely rule out the presence of a length bias in the microarray data, for example due to decreased accessibility of long transcripts for the microarray surface, and we note that care must be taken to control for length bias in any method that measures expression.
Suggestions: It would have been more useful to start with ChIP-seq datasets for TFs that have known motifs (derived from protein-binding microarray data, for example), and then evaluate the web tools on their ability to recover the known motifs.
Metabolomics data from breast cancer patients can be used in a similar way to gene expression microarray data, using, for example, hierarchical clustering and heat maps.
Our microarray data sets provide numerous examples of GSTP1-dependent gexpressionsion changes, and may therefore allow us to identify additional biomarkers, which correlate with GSTP1 activity.
Contrary to most other classification methods and due to the way data are represented through kernels, SVMs can tackle high dimensional data (for example microarray data).
For example, microarray data suggested that Cdkn1a response to TAM and EE were comparable, but through QRT-PCR EE induced an 8-fold response compared to a 3.5-fold induction by TAM.
Experimental tables containing, for example, microarray data, are clustered based on the Z-scores obtained using Fisher r-to-Z transformation of Pearson correlation coefficients calculating co-expression of the query gene with each gene in each experiment (data for each gene are averaged over multiple probes).
For example, microarray data showing a 4-fold change derived from low signal intensities may have no statistical significance whereas a 1.4 fold change derived from strong signal intensities may be highly significant in terms of reflecting actual changes in mRNA concentration within a biological sample.
Additionally a web-based consolidation framework that encompasses all three methods discussed in this paper, Pathway Distiller (http://cbbiweb.uthscsa.edu/PathwayDistiller), is established to allow researchers access to the methods and example microarray data described in this manuscript, and the ability to analyze their own gene list by using our unique consolidation methods.
