A NEW METABOLOMICS ANALYSIS TECHNIQUE: STEADY-STATE METABOLIC NETWORK DYNAMICS ANALYSIS


Cakmak A. , Qi X., Cicek A. E. , Bederman I., Henderson L., Drumm M., ...More

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, vol.10, no.1, 2012 (Journal Indexed in SCI) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 10 Issue: 1
  • Publication Date: 2012
  • Doi Number: 10.1142/s0219720012400033
  • Title of Journal : JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY

Abstract

With the recent advances in experimental technologies, such as gas chromatography and mass spectrometry, the number of metabolites that can be measured in biofluids of individuals has markedly increased. Given a set of such measurements, a very common task encountered by biologists is to identify the metabolic mechanisms that lead to changes in the concentrations of given metabolites and interpret the metabolic consequences of the observed changes in terms of physiological problems, nutritional deficiencies, or diseases. In this paper, we present the steady-state metabolic network dynamics analysis (SMDA) approach in detail, together with its application in a cystic fibrosis study. We also present a computational performance evaluation of the SMDA tool against a mammalian metabolic network database. The query output space of the SMDA tool is exponentially large in the number of reactions of the network. However, (i) larger numbers of observations exponentially reduce the output size, and (ii) exploratory search and browsing of the query output space is provided to allow users to search for what they are looking for.