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DOI: 10.4230/OASIcs.GCB.2012.1

ModeScore: A Method to Infer Changed Activity of Metabolic Function from Transcript Profiles

Authors: Andreas Hoppe and Hermann-Georg Holzhütter

Published in: OASIcs, Volume 26, German Conference on Bioinformatics 2012

Abstract

Genome-wide transcript profiles are often the only available quantitative data for a particular perturbation of a cellular system and their interpretation with respect to the metabolism is a major challenge in systems biology, especially beyond on/off distinction of genes. We present a method that predicts activity changes of metabolic functions by scoring reference flux distributions based on relative transcript profiles, providing a ranked list of most regulated functions. Then, for each metabolic function, the involved genes are ranked upon how much they represent a specific regulation pattern. Compared with the naïve pathway-based approach, the reference modes can be chosen freely, and they represent full metabolic functions, thus, directly provide testable hypotheses for the metabolic study. In conclusion, the novel method provides promising functions for subsequent experimental elucidation together with outstanding associated genes, solely based on transcript profiles.

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Andreas Hoppe and Hermann-Georg Holzhütter. ModeScore: A Method to Infer Changed Activity of Metabolic Function from Transcript Profiles. In German Conference on Bioinformatics 2012. Open Access Series in Informatics (OASIcs), Volume 26, pp. 1-11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@InProceedings{hoppe_et_al:OASIcs.GCB.2012.1,
  author =	{Hoppe, Andreas and Holzh\"{u}tter, Hermann-Georg},
  title =	{{ModeScore: A Method to Infer Changed Activity of Metabolic Function from Transcript Profiles}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{1--11},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{B\"{o}cker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2012.1},
  URN =		{urn:nbn:de:0030-drops-37134},
  doi =		{10.4230/OASIcs.GCB.2012.1},
  annote =	{Keywords: Metabolic network, expression profile, metabolic function}
}

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Documents authored by Holzhütter, Hermann-Georg

ModeScore: A Method to Infer Changed Activity of Metabolic Function from Transcript Profiles

Abstract

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