Types of inconsistencies caused by undifferentiated mRNA and proteins in the network representation. On both images A and C, inconsistencies occur on the node 'B'. The first example (A) is inconsistent because the product of gene expression, represented by node 'B' is a target of both transcriptional (TR) and post-translational (P-TR) regulations, which is not possible since transcriptional interactions should target mRNAs, while post-translational interactions target proteins. This inconsistency is removed by the differentiation between mRNAs (node 'mRNA_B') and proteins (node 'B') as shown on image B. The second type of inconsistency (C) is caused by the association of experimental data on variation in mRNA with a node which should represent a protein because it is a target of post-translational regulations. This inconsistency can also be avoided if mRNAs and proteins are distinguished in the network (D).
Baumuratova et al. BMC Systems Biology 2010 4:146 doi:10.1186/1752-0509-4-146