Fig. 5

Basic RAS2 AF/LO Network Augmented with AT and CI Nodes. Shown is the AF/LO network containing only LOs involving the gene RAS2 from S. cerevisiae and all AFs involved in these LOs (basic RAS2 network). LO nodes are labelled with the lifespan change value, if available. “n/a” indicates a missing value. The qualitative lifespan effect is also encoded in the LO node and edge colour, according to the colour scheme below. a There are 11 LOs were only the RAS2 gene is involved. But the lifespan change values seem to be contradictory: 6 times an increased lifespan versus 5 times a decreased lifespan. Network size: 16 nodes, 15 edges; Layout calculation: 3dFL algorithm with standard parameters; b In addition to the nodes in part a, ATs and CIs from these LOs are included. ATs describe the experimental changes applied to genes, for example deletion or overexpression. They were unified according to Table 3. Citations resemble the publications from which the LOs were extracted, represented by the corresponding PubMed IDs. In contrast to the pure basic network in part A, most of the possible contradictions between the lifespan changes are resolved immediately. In all cases with reduced lifespan the RAS2 gene was deactivated (AT: loss of function). In 5 of 6 cases with increased lifespan it was overexpressed instead (AT: overexpression). So the differences here fit to the expectation that overexpression of a gene has the opposite effect compared to loss of function. This leaves a single contradiction. One can see that the remaining contradictory LO was extracted from a different publication than the others. In general, this could be a hint that the experiments might have been performed under different conditions, which were not recorded during the extraction of the LO. Network size: 23 nodes, 44 edges; Layout calculation: 3dFL algorithm with standard parameters; Color scheme (a, b): AF - gene, AF - other factor, LO - increased lifespan, LO - decreased lifespan, AT, CI