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Therefore, a possible extension of the method could be to take into account noisy data, i.e. to deal with a level of confidence for the roles of discriminating compounds and non-discriminating compounds.
A natural idea is to try to link all discriminating compounds through chains of reactions.
Our approach is a subgraph extraction technique in which we want to find maximal directed acyclic subgraphs (DAGs) whose set of sources and targets are discriminating compounds.
Furthermore, this global view of the discriminating compounds links the sulfur metabolism to non-sulfur amino acids and other metabolites through intermediates of the central metabolism.
The simplest idea one may think of is to highlight the set of metabolites identified in the experiment that have significantly changed their concentration, let us call them discriminating compounds, and then to visually analyze their interconnections.
This more local view of the behavior of the metabolic network of yeast in this stress condition may be contrasted with the second analysis, where the whole list of discriminating compounds was considered.
Similar(31)
Fraction 4 was further purified by HPLC to obtain 9 mg of the pure metabolite named herein harziaphilic acid (9; Table 1, Fig. 2), that represents the main discriminating compound in the M10-F36CF co-culture.
Besides, citrulline was identified as a discriminating compound in Madalinski et al. (2008), but was only indicated as putative, requiring more analysis for final identification.
In experiments with cytosolic and endoplasmic reticulum (ER) Ca2+ measurements and with the use of 10 μM La3+ as a discriminating compound, the RACE pathway accompanied by very moderate store depletion was suggested to be mainly responsible for histamine-induced Ca2+ entry into EA.hy926 cells (Jousset et al., 2008), which questions the relevance of SOCE.
Our comparative analysis was also able to discriminate compounds that are not reported to directly bind AR but instead are inhibitors of AR co-regulators.
The algorithm however is agnostic of atom types and cannot discriminate compounds with similar shape but distinct pharmacophoric features.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com