Barvkar et al. BMC Genomics 2012, 13:175 http://www.biomedcentral.com/1471-2164/13/175 Page 6 of 13 of UGTs to construct a heat map (Figure 3). Hierarchical clustering with Pearson correlation matrix highlighted co-expression of specific gene family members in specific tissue types. Only 60 of the 137 (43.79%) flax UGTs represented on the array showed expression evidence (Additional file 7). Three genes were highly expressed in seed stages S2 and S3 (averaged gene-level log2 value: LuUGT85R2 (11.11 and 11.30), LuUGT709E2 (10.57 and 10.76), and LuUGT709E3 (10.57 and 10.76), respectively; while one gene (LuUGT85Q3, averaged gene-level log2 value: 11.53) showed the highest expression in leaf tissue (Figure 3). The number of genes having higher expression in different tissues (averaged gene-level log2 values >6.96) varied from 14 (S1) to 24 (SOGC) (Additional file 7). Among the different tissues, SOGC had the largest num- ber of highly expressed genes, while S3 had the lowest (23%) (Additional file 7). Surprisingly, the two contrasting varieties, Drakkar and Belinka did not show any difference in the expression of these 60 UGTs (Figure 3). Expression profiling using RT-qPCR The RT-qPCR is currently the most accurate method for detecting differential gene expression. The 12 tissue types selected for UGT expression profiling cover all plant parts Figure 3 Expression levels for flax UGT genes in various tissues by microarray analysis. The RMA-normalized, average log2 signal values of flax UGTs in various tissues and seed developmental stages (listed at the top of heat map) were used for construction of the heat map. The left side of the heat map shows hierarchical clustering based on Pearson correlation matrix. The colour scale (representing log2 signal values) is shown at the top. Microarray data from stem outer tissues; vegetative stage (SOV), stem outer tissues, green capsule stage (SOGC), stem inner tissues; vegetative stage (SIV), stem inner tissues; green capsule stage (SIGC), leaves (L), roots (R), seeds, 10–15 DAF (S1), seeds, 20–30 DAF (S2) and seeds, 40–50 DAF (S3) were used for constructing the expression heat map.