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On the integration of protein-protein interaction networks with gene expression and 3D structural data: What can be gained?

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Abstract

The biological role of proteins has been analyzed from different perspectives, initially by considering proteins as isolated biological entities, then as cooperating entities that perform their function by interacting with other molecules. There are other dimensions that are important for the complete understanding of the biological processes: time and location. However a protein is rarely annotated with temporal and spatial information. Experimental Protein-Proteins Interaction (PPI) data are static; furthermore they generally do not include transient interactions which are a considerable fraction of the interactome of many organisms. One way to incorporate temporal and condition information is to use other sources of information, such as gene expression data and 3D structural data. Here we review work done to understand the insight that can be gained by enriching PPI data with gene expression and 3D structural data. In particular, we address the following questions: Can the dynamics of a single protein or of an interaction be accurately derived from these data? Can the assembly-disassembly of protein complexes be traced over time? What type of topological changes occur in a PPI network architecture over time?

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Authors and Affiliations

  1. IASI-CNR, Roma, Italy

    Paola Bertolazzi, Paola Paci & Daniele Santoni

  2. Department of Statistics, Purdue University, West-Lafayette, IN, USA

    Mary Ellen Bock

  3. College of Computing, Georgia Institute of Technology, Atlanta, GA, USA

    Concettina Guerra

Authors
  1. Paola Bertolazzi
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  2. Mary Ellen Bock
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  3. Concettina Guerra
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  4. Paola Paci
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  5. Daniele Santoni
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Corresponding author

Correspondence to Concettina Guerra.

Additional information

Contribution to the Focus Point “Pattern Recognition Tools for Proteomics” edited by V. Cantoni.

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Bertolazzi, P., Bock, M.E., Guerra, C. et al. On the integration of protein-protein interaction networks with gene expression and 3D structural data: What can be gained?. Eur. Phys. J. Plus 129, 134 (2014). https://doi.org/10.1140/epjp/i2014-14134-y

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  • DOI: https://doi.org/10.1140/epjp/i2014-14134-y

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