Fig. 4

Screen shot of the GeneExplore (Degust) browser and subsequent result pages. a the Arabidopsis time-series data-set is shown here as an example, displaying transcripts that are up-regulated in S samples but down-regulated in SL samples (Top panel). The user can select which samples they wish to see with the checkboxes in the top left of screen along with the method of analysis (voom/limma, edgeR, or voom). In the top right, the user can control the rendering and thresholds of using the options dialog. All genes that match filters above are shown in a heat-map, which clusters genes with similar levels of expression (Middle panel). Running the mouse-over each gene highlights it in the plots above. Table showing all matching genes in tabular format with the expression levels for each sample, false discovery rate and any extra annotation columns provided in the data-set (Lower panel). In the top centre the user can limit genes by using 1 of 3 interactive plots, and the parallel coordinates plot allows the user to limit genes by their log fold gene expression (per sample). b Example of an MA plot. Users can limit genes by drawing a box around genes on the on the MA plot; the two samples used for the MA plot are specified in the Options dialog (top right). c An MDS plot showing groupings of the individual replicates of each sample. Data is from transcriptome of Arabidopsis seed during germination [20]