Fig. 7

Candidate Gene Identification - Overview. Shown is an overview of the visualisation strategy to identify new candidate genes of C. elegans for inclusion in the database AgeFactDB. For each part of this figure there is also a larger version available, as an individual figure with a more detailed description (Additional file 2: Figures S7–S15). In the combined colour scheme below it is indicated which colours are applicable to which part. The layout was calculated in step 1 and 2 using the FMMM algorithm. Throughout step 3 to 8 the layout from step 2 was used, to facilitate tracking the changes. Instead of changing the layout, nodes were hidden, or node attributes like colour or size were changed during these steps. In step 9 a new layout was calculated using the FR algorithm. a Step 1: the complete AF/LO network of C. elegans with 675 subnetworks as starting point (Additional file 2: Figure S7); b Step 2: augmentation with KEGG pathway and gene nodes, based on cross-linking information from the BioSystems database (Additional file 2: Figure S8); c Step3: visual transfer of lifespan change information from LO nodes to AF nodes (Additional file 2: Figure S9); d Step 4: reduction of network complexity by hiding all LO nodes (Additional file 2: Figure S10); e Step 5: first reduction of candidate gene number by applying a minimum lifespan change limit (Additional file 2: Figure S11); f Step 6: second reduction of candidate gene number by selecting only genes connected to at least 6 KEGG pathway nodes; final selected candidate genes are marked by a halo (Additional file 2: Figure S12); g Step 7: zoom into the area with most of the candidate genes; Table 4 lists the final selected candidate genes and their literature analysis results (Additional file 2: Figure S13); h Step 8: focus on candidate gene enol-1 by zooming and selective node display (Additional file 2: Figure S14); i Step 9: visualisation of the basic pathway network of candidate gene enol-1, augmented by AFs with data transferred from their LOs (Additional file 2: Figure S15); Color scheme: AF - gene (a,b), AF - compound (a), AF - other factor (a), AF - LOs with increased lifespan (opaque: only, transparent: ≥80%; c,d,e,f,g,h,i), AF - LOs with decreased lifespan (opaque: only, transparent: ≥80%; c,d,i), AF - LOs with highly mixed lifespan changes (increased and decreased >20%; c,d,e,f,g,h,i), LO - increased lifespan (a,b,c small), LO - decreased lifespan (a,b,c small), LO - unchanged lifespan (a,b,c), KEGG pathway (b,c,d,e,f,g,h,i), gene (from pathway and not in AgeFactDB; b,c,d,e,f,g,h), selected candidate gene (f,g,h,i)