Figure 2
From: The space of enzyme regulation in HeLa cells can be inferred from its intracellular metabolome
The k-cone space of HaCaT and HeLa cells.
(A) Missing data are imputed within or across conditions using the measured concentrations. The “+” sign denotes newly imputed values. Only metabolites completely lacking from measurements are obtained from the HMDB database. Enzyme activities in a disease state are given by a distinct transformation of enzyme activities from a healthy reference, composed of a transformation matrix T, which transforms the entire k-cone space and is given by metabolome data alone and a weight matrix W, which maps the distinct points of enzyme activities in the k-cone spaces and requires fluxome data. For visualization purposes, the k-cone spaces were reduced to the two dimensions explaining the highest variance. (B) Projection of k-cone spaces for HaCaT metabolome measurements (blue) and HeLa (red). The axes correspond to the two largest eigenvectors of the entire space and the annotations denote reactions with the highest absolute loadings in those eigenvectors. Arrows denote the clusters of basis vectors of the respective k-cones and shaded areas denote the space within the k-cone; thus, all points falling in this area denote feasible enzyme activities (3 measurements for each cell line). The relative error of the dimension reduction is 6.7%. The mean distance within arrow clusters is 0.13. (C) K-cone spaces for only those reactions whose mass-action terms changed at least by a factor of 2. The relative error of the projection was 6.9% and the mean distance within arrow clusters was 2.8e-5.
