A coherent framework for multiresolution analysis of biological networks with "memory": Ras pathway, cell cycle, and immune system

Paolo Emilio Barbano, Marina Spivak, Jiawu Feng, Marco Antoniotti, Bud Mishra

Research output: Contribution to journalArticle

Abstract

Various biological processes exhibit characteristics that vary dramatically in response to different input conditions or changes in the history of the process itself. One of the examples studied here, the Ras-PKC-mitogen-activated protein kinase (MAPK) bistable pathway, follows two distinct dynamics (modes) depending on duration and strength of EGF stimulus. Similar examples are found in the behavior of the cell cycle and the immune system. A classification methodology, based on time-frequency analysis, was developed and tested on these systems to understand global behavior of biological processes. Contrary to most traditionally used statistical and spectral methods, our approach captures complex functional relations between parts of the systems in a simple way. The resulting algorithms are capable of analyzing and classifying sets of time-series data obtained from in vivo or in vitro experiments, or in silico simulation of biological processes. The method was found to be considerably stable under stochastic noise perturbation and, therefore, suitable for the analysis of real experimental data.

Original languageEnglish (US)
Pages (from-to)6245-6250
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume102
Issue number18
DOIs
StatePublished - May 3 2005

Keywords

  • Ras-PKC-mitogen-activated protein kinase (MARK) pathway
  • Systems biology
  • Time-frequency analysis

ASJC Scopus subject areas

  • General

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