Fatty acid biosynthesis model and pathway distance calculation method. A: De novo synthesis of fatty acids with initial SCD-dependent desaturations (left), and the ω-3 and ω-6 poly-unsaturated fatty acid pathways (middle and right). Note that we omitted the specific positions of each double-bond since the mass-spectrometry technique in our study does not resolve positional information. B: Exemplary distance calculation on two lyso-PCs. We projected lipid side chain compositions onto the respective fatty-acid biosynthesis reactions. Reaction reversibility is not taken into account in our calculation, i.e. distances are always symmetric. C: If no known pathway connection between two fatty acids exists, we assign a formal distance of infinity. D: For phospholipids that contain two fatty acid residues we need to take into account all combinatorial variants. We here show three variants for the connection between PC aa C38:4 and PC aa C38:5. In these examples, PC aa C38:4 could either consist of C18:0+C20:4 or C16:0+C22:4, while PC aa C38:5 could be C18:0+C20:5 or C16:0+C22:5. The shortest possible distance, one in this case, will be used for further calculations.
Krumsiek et al. BMC Systems Biology 2011 5:21 doi:10.1186/1752-0509-5-21