Integrative Approaches to Elucidate and Analyze Protein Interaction and Signaling Networks

Sergio De La Fuente Van Bentem*, Alberto De La Fuente, Heribert Hirt

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

Abstract

The introduction of high-throughput techniques that generate large data sets has urged the development of systematic approaches to interpret these data and transform them into comprehensible models. The formulation of network models from global protein studies is essential to understand the functioning of organisms. Currently, several network concepts have emerged in the field of proteomics. It is important to highlight the differences between these concepts, since different representations allow distinct insights into functional organization. One such concept is the Protein Interaction Network (PIN), which contains proteins as nodes and undirected edges representing binding events observed in large-scale protein-protein interaction studies. A second concept is the Protein Signaling Network (PSN), in which the nodes correspond to levels of post-translationally modified forms of proteins and directed edges to causal effects through post-translational modification, such as phosphorylation. The plant field has recently employed high-throughput methods such as mass spectrometry and protein chips to study protein-protein interactions and signaling pathways. Data from nonplant model systems have been used to predict the first global protein interaction networks in plants. These data can be integrated with data collected by other large-scale approaches, such as metabolomics and transcriptomics. Such integrative approaches should aid in understanding the flexibility of plant responses triggered by a frequently changing environment.

Original languageEnglish (US)
Title of host publicationPlant Stress Biology
Subtitle of host publicationFrom Genomics to Systems Biology
PublisherWiley-VCH
Pages227-248
Number of pages22
ISBN (Print)9783527322909
DOIs
StatePublished - Jan 22 2010

Keywords

  • Complex network analysis
  • Integrative approach
  • Protein interaction network
  • Protein signaling network
  • Quantitative proteomics
  • Tandem affinity purification

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

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