The solutions have
been obtained with 5 different parameters settings, all of which include thermodynamic realizability [45] with concentration bound hard bounds. The first solution series is computed without any implied scoring scheme, the second with flux minimization, the rest additionally with soft bounds for the concentrations. Among the different solutions, the Inhibitors,research,lifescience,medical one with the fewest used reactions is used. Reference flux distributions with no associated genes are removed, 987 remain. After the computation each mode Mk = (mi(k))i = 1…n is normalized, i.e., divided by Σi Ik |mi(k)| , where mi(k) is the flux rate through reaction i, and n the number of reactions. 4.4. ModeScore Method The core of the ModeScore method [15] is the calculation of an amplitude value for a reference mode and a pair of transcript profiles, and additionally for each gene a contribution score, as follows: Let the k-th reference mode be denoted by Mk = (mi(k))i = 1…n and the relative Inhibitors,research,lifescience,medical expression H 89 profile by V = (vi)i = 1…n, where vi is the difference of the log2 values of the transcript abundances of one state and a reference state. Then the score of the mode is where and λ is chosen such that Score(Mk, V) is maximal, see [15] for details on the optimization procedure. The non-negative numbers ωi are the weight adjustments Inhibitors,research,lifescience,medical to increase the influence of reactions with stoichiometric factors larger
than one (except protons). For lumped reactions, ωi is set to the number of individual conversions. For spontaneous reactions, it is set to zero. For a complete list, see Supplementary file 7. To evaluate a function (i.e., a reference flux distribution) with respect Inhibitors,research,lifescience,medical to two expression profiles, the amplitude, calculated as 1/λ is used. The amplitude is compatible to the log2 expression change, i.e., if all genes are changed by the same amount α the amplitude would be α. Rather than averaging the transcript changes of all genes related to a function, the amplitude shows the most consistent pattern of synchronous regulation. The Score(Mk, V) is of lesser importance; it Inhibitors,research,lifescience,medical serves as a significance
found score where values close to 1 indicate an unequivocal decision and low values less than 0.2 show an ambiguous pattern. To evaluate the contributions of the individual genes, the scorei(mi(k), vi) values are used, where a high scorei(mi(k),vi) shows a high influence of the gene on the whole function’s evaluation. The table in Supplementary file 5 are sorted by the combined scorei(mi(k), vi) adjusted with the weight parameters wi. 4.5. ModeScore Analysis The functions with very high and low amplitudes (about 20 each) of the profile comparisons 1 h vs. 24 h for each untreated (A) and treated samples (B) and the control vs. TGFβ comparison for 24 h (C) have been analyzed for their functional relevance, see Supplementary file 5.