D. Santoni, A. Swiercz, A. Zmienko, M. Kasprzak, M. Blazewicz, P. Bertolazzi, G. Felici
"An integrated approach (CLuster Analysis Integration Method) to combine
expression data and protein-protein interaction networks in agrigenomics:
application on Arabidopsis thaliana"
OMICS: A Journal of Integrative Biology
18 (2014) 155-165.
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— The final publication is available at Mary Ann Liebert, Inc. via
http://online.liebertpub.com/doi/abs/10.1089/omi.2013.0050
Abstract:
Experimental co-expression data and protein-protein interaction networks are
frequently used to analyze the interactions among genes or proteins. Recent
studies have investigated methods to integrate these two sources of information.
We propose a new method to integrate co-expression data obtained through DNA
microarray analysis (MA) and protein-protein interaction (PPI) network data,
and apply it to Arabidopsis thaliana. The proposed method identifies
small subsets of highly interacting proteins. Based on the analysis of the
basis of co-localization and mRNA developmental expression, we show that these
groups provide important biological insights; additionally, these subsets are
significantly enriched with respect to KEGG Pathways and can be used to predict
successfully whether proteins belong to known pathways. Thus, the method is
able to provide relevant biological information and support the functional
identification of complex genetic traits of economic value in plant
agrigenomics research. The method has been implemented in a prototype software
tool named CLAIM (CLuster Analysis Integration Method) and can be downloaded
from http://bio.cs.put.poznan.pl/research_fields. CLAIM is based on the
separate clustering of MA and PPI data; the clusters are merged in a special
graph; cliques of this graph are subsets of strongly connected proteins. The
proposed method was successfully compared with existing methods. CLAIM appears
to be a useful semi-automated tool for protein functional analysis and warrants
further evaluation in agrigenomics research.
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3 Feb 2014