A framework for mapping, visualisation and automatic model creation of signal-transduction networks.
Artikel i vetenskaplig tidskrift, 2012

Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal-transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system.

Models

enzymology

Software

Databases

Molecular

genetics

Factual

methods

Saccharomyces cerevisiae

Systems Biology

growth & development

Protein Interaction Mapping

Metabolic Networks and Pathways

Empirical Research

Computer Simulation

Signal Transduction

physiology

Författare

Carl Fredrik Tiger

Göteborgs universitet

Falko Krause

Gunnar Cedersund

Göteborgs universitet

Robert Palmér

Edda Klipp

Stefan Hohmann

Göteborgs universitet

Hiroaki Kitano

Marcus Krantz

Göteborgs universitet

Molecular Systems Biology

17444292 (eISSN)

Vol. 8 artikel nr 578-

Ämneskategorier

Biokemi och molekylärbiologi

DOI

10.1038/msb.2012.12

PubMed

22531118

Mer information

Skapat

2017-10-10