کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
4499977 1624018 2015 8 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Generic flux coupling analysis
ترجمه فارسی عنوان
تجزیه و تحلیل همبستگی شونده
کلمات کلیدی
شبکه متابولیک، تجزیه و تحلیل جفتی، مدل کیفی، محدودیت ترمودینامیکی
موضوعات مرتبط
علوم زیستی و بیوفناوری علوم کشاورزی و بیولوژیک علوم کشاورزی و بیولوژیک (عمومی)
چکیده انگلیسی


• We extend flux coupling analysis (FCA) to arbitrary qualitative pathway models.
• We develop an efficient generic FCA algorithm.
• We derive an efficient method for FCA with loop-law thermodynamic constraints (tFCA).
• Loop-law thermodynamic constraints strengthen results obtained by standard FCA.

Flux coupling analysis (FCA) has become a useful tool for aiding metabolic reconstructions and guiding genetic manipulations. Originally, it was introduced for constraint-based models of metabolic networks that are based on the steady-state assumption. Recently, we have shown that the steady-state assumption can be replaced by a weaker lattice-theoretic property related to the supports of metabolic fluxes. In this paper, we further extend our approach and develop an efficient algorithm for generic flux coupling analysis that works with any kind of qualitative pathway model. We illustrate our method by thermodynamic flux coupling analysis (tFCA), which allows studying steady-state metabolic models with loop-law thermodynamic constraints. These models do not satisfy the lattice-theoretic properties required in our previous work. For a selection of genome-scale metabolic network reconstructions, we discuss both theoretically and practically, how thermodynamic constraints strengthen the coupling results that can be obtained with classical FCA. A prototype implementation of tFCA is available at http://hoverboard.io/L4FC.


• testBlocked(reaction r)
• testCoupled(reaction r, reaction s)Figure optionsDownload as PowerPoint slide

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Mathematical Biosciences - Volume 262, April 2015, Pages 28–35
نویسندگان
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