Journal Article

In response to ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’

Karoline Faust, Didier Croes and Jacques van Helden

in Bioinformatics

Volume 25, issue 23, pages 3202-3205
Published in print December 2009 | ISSN: 1367-4803
Published online September 2009 | e-ISSN: 1460-2059 | DOI: https://dx.doi.org/10.1093/bioinformatics/btp557
In response to ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’

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Motivation: In their article entitled ‘Can sugars be produced from fatty acids? A test case for pathway analysis tools’ de Figueiredo and co-authors assess the performance of three pathway prediction tools (METATOOL, PathFinding and Pathway Hunter Tool) using the synthesis of glucose-6-phosphate (G6P) from acetyl-CoA in humans as a test case. We think that this article is biased for three reasons: (i) the metabolic networks used as input for the respective tools were of very different sizes; (ii) the ‘assessment’ is restricted to two study cases; (iii) developers are inherently more skilled to use their own tools than those developed by other people. We extended the analyses led by de Figueiredo and clearly show that the apparent superior performance of their tool (METATOOL) is partly due to the differences in input network sizes. We also see a conceptual problem in the comparison of tools that serve different purposes. In our opinion, metabolic path finding and elementary mode analysis are answering different biological questions, and should be considered as complementary rather than competitive approaches.

Contact: kfaust@ulb.ac.be

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  2847 words. 

Subjects: Bioinformatics and Computational Biology

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