GATE: Software for the Analysis and Visualization of High- Dimensional Time-series Expression Data

A series of Affymetrix mouse 430 expression set microarrays were obtained for each shRNAi knock-down time-series (hereafter referred to as experiment). For this analysis we considered microarray time-course data obtained at days 0, 2, 4, 6 for each experiment. Thus, we considered 7 microarray time-courses, each of length 4. Full MIAME compliant datasets are available at first normalized using MAS5.0 software and log 2 was taken. Only probe sets matching well annotated genes were considered for further analysis. Probe sets recognizing multiple transcripts were excluded from analysis, as were those which cross-hybridize to alternative non-related sequences. In the case that multiple probes matched the same gene, the average expression across all probe sets was taken at each time-point. In order to exclude false positive results due to low expression levels we also excluded probe sets which had below median (for the entire experiment) expression for all time-points. We also excluded from further analysis, those time-series which had no present calls as determined by MAS5.0 software. Finally, we selected for further analysis those genes which had at least a twofold change in expression at some time point relative to the corresponding time-point in an empty vector control series. This gave a set of between 429 and 936 well-annotated genes per experiment for further investigation using GATE. unique, well-annotated, genes in total. This gene-set includes a variety of core ES cell associated genes such as Nanog, Pou5f1,