To perform Upstream Regulator Analysis (URA), firstly the <*ura_databases*> database was filtered to include only genes that are also in both the normalised expression file and the background file (the expression set). Next the database was filtered to include only upstream regulator gene sets with between <*ura_min_set_size*> and <*ura_max_set_size*> valid genes. For each each set of candidate genes (i.e. all significant, all upregulated and all downregulated genes) and only upstream regulator gene set combination a hypergeometric gene set analysis was performed (as described above) and a URA analysis performed as http://pages.ingenuity.com/rs/ingenuity/images/0812%20upstream_regulator_analysis_whitepaper.pdf. Gene sets with an adjusted p-value of <*ura_padj*>, an absolute log2fold enrichment above <*ura_log2fold*>, and an absolute activation z-score above <*ura_zscore*> were considered significant.

