Figure 3

Scheme of constructing ‘differential expression network (DEN)’.

The new form of network named DEN is based on both molecular network (e.g. PPI network) and gene expression profiles to characterize biological process (Fig. 2A), in contrast to traditional ‘differential genes’ (DG; Fig. 2C) or ‘differential network’ (DN; Fig. 2D). DEN is composed of ‘non-differential interactions’ and ‘differential interactions’. In Fig. 2 B, the gene is labeled in green if it is down regulated compared to Case or Control, while red if up regulated. The gene is labeled in black if there is no significant difference between Case and Control. In Fig. 2 C–G, the gene is labeled in green if its differential value is negative, while red if positive. The gene is labeled in black if its differential value is around zero. As a result, DEN is constructed for each tissue. In addition, the comparison of our DEN scheme with traditional schemes is also can be shown. DG only considers those individual genes whose expressions have significant differences under two different conditions, while DN is composed of the differential interactions that have significant differences in different states, without consideration of disease-related non-differential interactions.