Figure 4

Screenshot of the report following importing and processing of the Bioconductor estrogen contrast data in Confero using Galaxy. The report shows 1) whether contrast data have been correctly imported and processed (several checks during the mapping and collapsing process reported at the top of the document (“Check/Map/Collapse Contrast Dataset Report”), 2) information on the gene sets that have been automatically extracted from each contrast and stored (UP, DN, and AR gene sets) in the Confero DB (“Gene Set Report”). As example (see also Figure 5), 169, 105 and 274 most significantly up- , down- and all-regulated genes (FDR<0.05) were respectively extracted as gene sets UP, DN and AR from the contrast data “Estro10” (comparison of gene expression levels of estrogen vs control samples collected at 10h).