Figure 1
Analyses of SAM gene lists. A. Venn diagram of SAM results. SAM results from six r-group comparisons are presented for the DePreter and McArdle/Wilzén data sets. # cases = Total number of cases included in each comparison from each data set; # overlapping genes = Total number of genes overlapping between the original SAM gene lists (1000 genes from each direction) from data set 1 and 2, constituting the SAMintersect gene lists; # significant genes = Total number of overlapping significant genes (combined p-value) using a cut-off of p < 6.25E-06, which correspond to a Bonferroni corrected p-value of p < 0.05; # genes FC > 5 = Total number of overlapping genes showing a combined fold change (FC) above 5 in each comparison. B. Venn diagram of GO functional themes. The Biological Networks Gene Ontology (BiNGO) tool in Cytoscape was utilized to map the predominant functional themes of the SAM gene lists. The most dominating Gene Ontology (GO) terms from each SAM comparison are presented from two differential expression directions; "up" (left panel) or "down" (right panel). Upper panel: r-group comparisons from all three data sets; data set 1 (DePreter), data set 2 (McArdle/Wilzén), and data set 3 (Wang). Lower panel: Histopathology group comparisons in data set 4 (Versteeg) The full GO search results are presented in Additional file 3. C. Gene network frequencies. The heat map table represents the percentage of network genes out of the total number of genes in the gene networks (marked in grey). The total number of genes in the SAM gene lists are presented to the right. The upper panel “Data sets 1 & 2_comb” represents combined intersect gene lists from the two data sets, and the other panels represents gene lists from the 1000 most differentially expressed genes in each direction.