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{Ames:2013:10.1371/journal.pone.0062670,
author = {Ames, RM and Macpherson, JI and Pinney, JW and Lovell, SC and Robertson, DL},
doi = {10.1371/journal.pone.0062670},
journal = {PLoS One},
title = {Modular biological function is most effectively captured by combining molecular interaction data types.},
url = {http://dx.doi.org/10.1371/journal.pone.0062670},
volume = {8},
year = {2013}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - Large-scale molecular interaction data sets have the potential to provide a comprehensive, system-wide understanding of biological function. Although individual molecules can be promiscuous in terms of their contribution to function, molecular functions emerge from the specific interactions of molecules giving rise to modular organisation. As functions often derive from a range of mechanisms, we demonstrate that they are best studied using networks derived from different sources. Implementing a graph partitioning algorithm we identify subnetworks in yeast protein-protein interaction (PPI), genetic interaction and gene co-regulation networks. Among these subnetworks we identify cohesive subgraphs that we expect to represent functional modules in the different data types. We demonstrate significant overlap between the subgraphs generated from the different data types and show these overlaps can represent related functions as represented by the Gene Ontology (GO). Next, we investigate the correspondence between our subgraphs and the Gene Ontology. This revealed varying degrees of coverage of the biological process, molecular function and cellular component ontologies, dependent on the data type. For example, subgraphs from the PPI show enrichment for 84%, 58% and 93% of annotated GO terms, respectively. Integrating the interaction data into a combined network increases the coverage of GO. Furthermore, the different annotation types of GO are not predominantly associated with one of the interaction data types. Collectively our results demonstrate that successful capture of functional relationships by network data depends on both the specific biological function being characterised and the type of network data being used. We identify functions that require integrated information to be accurately represented, demonstrating the limitations of individual data types. Combining interaction subnetworks across data types is therefore essential for fully understanding the comple
AU  - Ames,RM
AU  - Macpherson,JI
AU  - Pinney,JW
AU  - Lovell,SC
AU  - Robertson,DL
DO  - 10.1371/journal.pone.0062670
PY  - 2013///
TI  - Modular biological function is most effectively captured by combining molecular interaction data types.
T2  - PLoS One
UR  - http://dx.doi.org/10.1371/journal.pone.0062670
UR  - https://www.ncbi.nlm.nih.gov/pubmed/23658761
VL  - 8
ER  -
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