Figure 3

A) Scatterplot of tm- and ts-scores of DMD patient (number 4) when compared against healthy striated muscle. On the x-axis are tm-scores of the patient and on the y-axis are ts-scores of the patient. As explained in the figure 1D, upper right corner (high tm- and ts-scores) indicate genes having muscle specific expression and the query sample had expression level matching that. In this case there is clearly a group of genes having expression level assumed and specific for muscle and for this part the patients transcriptomic profile resembles healthy striated muscle. On the lower left corner are the genes (low tm- and ts scores) having muscle specific expression level (ts-score deviating from zero) but the query sample did not have expression level matching it. Thus these genes are potentially related to DMD. Eight a priori known DMD related genes are highlighted in red while novel gene in DMD (SAMD4A) is highlighted in green. SAMD4A has extremely muscle specific expression level but the query sample did not have expression matching it. B) Visualization of the normalized expression levels of selected genes from ten Duchenne Muscular Dystrophy samples in relation to the expression levels of these genes across all 44 normal tissue types. The green boxplot data display statistical data on gene expression for each of the normal tissue types (according to http://www.genesapiens.org), with the data from the 10 individual DMD samples added to the far right. Patients illustrated in figure 3 are colored red. MYH3, MYH7 and MYH8. MYH3 and MYH8 (left panel) are muscle contraction genes, whose expression is discordant for DMD tissue in patients 3 and 4. DMD samples show dramatic differences both between the patients and healthy striated muscle for the levels of expression of these genes. On the right panel are boxplots of genes C1S, C3, C1QA, representing key components of the complement mediated immunity process, whose expression values are different both between the patients and the healthy striated muscle. CLTCL1 is an interesting gene, whose expression is lost in 6 out of 10 patients.