Screen shots of ExpressionPlot 2way plot and table_browser. (a) 2way plot of human tissue panel RNA-Seq data  showing brain gene expression on the y-axis and average expression in all other tissues (pooled) on the x-axis. Blue points correspond to genes significantly higher (P ≤ 10-4, fold change ≥20, 370 points) in brain relative to the other tissues; green points correspond to significantly lower. (b) 2way plot showing cassette exon usage (inclusion:skip read ratios) instead of gene levels in the same data set. The heavy lobe above the diagonal corresponds to exons with zero skipping reads in the brain, and the lighter lobe below the diagonal corresponds to exons with zero skipping reads in all other tissues. Although the P-values are still valid, in these regimes the inclusion:skip ratio statistic is less precise. (c) Partial screen shot of table browser showing brain-enriched cassette exons in the same data set. The context menu was triggered by the mouse clicking on the row for CLTA (clathrin, light chain A) and offers the user links to open the seqview genome browser tool in a window covering either the entire gene or just the alternative exon. In either case the exon will be automatically highlighted (Figure 5).
Friedman and Maniatis Genome Biology 2011 12:R69 doi:10.1186/gb-2011-12-7-r69