Imperial College London
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DrJohnPinney

Central Faculty, Graduate School

Teaching Fellow- Data Science Skills Leader
 
 
 
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Contact

 

+44 (0)20 7594 8629j.pinney

 
 
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Location

 

327Sherfield BuildingSouth Kensington Campus

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Summary

 

Publications

Citation

BibTex format

@article{Pinney:2007:10.1073/pnas.0706339104,
author = {Pinney, JW and Amoutzias, GD and Rattray, M and Robertson, DL},
doi = {10.1073/pnas.0706339104},
journal = {Proc Natl Acad Sci U S A},
pages = {20449--20453},
title = {Reconstruction of ancestral protein interaction networks for the bZIP transcription factors.},
url = {http://dx.doi.org/10.1073/pnas.0706339104},
volume = {104},
year = {2007}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - As whole-genome protein-protein interaction datasets become available for a wide range of species, evolutionary biologists have the opportunity to address some of the unanswered questions surrounding the evolution of these complex systems. Protein interaction networks from divergent organisms may be compared to investigate how gene duplication, deletion, and rewiring processes have shaped the evolution of their contemporary structures. However, current approaches for comparing observed networks from multiple species lack the phylogenetic context necessary to reconstruct the evolutionary history of a network. Here we show how probabilistic modeling can provide a platform for the quantitative analysis of multiple protein interaction networks. We apply this technique to the reconstruction of ancestral networks for the bZIP family of transcription factors and find that excellent agreement is obtained with an alternative sequence-based method for the prediction of leucine zipper interactions. Further analysis shows our probabilistic method to be significantly more robust to the presence of noise in the observed network data than a simple parsimony-based approach. In addition, the integration of evidence over multiple species means that the same method may be used to improve the quality of noisy interaction data for extant species. The ancestral states of a protein interaction network have been reconstructed here by using an explicit probabilistic model of network evolution. We anticipate that this model will form the basis of more general methods for probing the evolutionary history of biochemical networks.
AU  - Pinney,JW
AU  - Amoutzias,GD
AU  - Rattray,M
AU  - Robertson,DL
DO  - 10.1073/pnas.0706339104
EP  - 20453
PY  - 2007///
SP  - 20449
TI  - Reconstruction of ancestral protein interaction networks for the bZIP transcription factors.
T2  - Proc Natl Acad Sci U S A
UR  - http://dx.doi.org/10.1073/pnas.0706339104
UR  - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=18077348&query_hl=1
VL  - 104
ER  -
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