Response to comment on 'Can sugars be produced from fatty acids ? A test case for pathway analysis tools'

摘要

The main points of criticism by Faust et al. (2009) concerning the work in de Figueiredo et al. (2009a) are the following: the cases presented are biased; different tools should be supplied with the same input networks; the number of study cases should be representative; and tools should be evaluated by neutral assessors. We think that the models in de Figueiredo et al. (2009a) illustrate concrete biological problems that are very well documented. In particular, the conversion of fatty acids into sugars was not so trivial to be answered and is historically relevant (cf. Weinman et al., 1957). Today, many biochemistry textbooks dedicate at least one paragraph explaining why there is no net conversion of acetyl-CoA to glucose via the tricarboxylic acid cycle in vertebrates (cf. Stryer, 1995; Nelson and Cox, 2000; Voet and Voet, 2004). Thus, new tools for metabolic pathway prediction have to be able to answer these problems correctly.