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The determination of protein functions is one of the most challenging problems of the post-genomic era. The sequencing of entire genomes and the possibility to access genes co-expression patterns has moved the attention from the study of single proteins or small complexes to that of the entire proteome. In this context, the search for reliable methods for proteins function assignment is of uttermost importance. Previous approaches to deduce the unknown function of a class of proteins have exploited sequence similarities or clustering of co-regulated genes, phylogenetic profiles, protein-protein interactions, and protein complexes. We propose to assign functional classes to proteins from their network of physical interactions, by minimizing the number of interacting proteins with different categories. The function assignment is made on a global scale and depends on the entire connectivity pattern of the protein network. Multiple functional assignments are made possible as a consequence of the existence of multiple equivalent solutions. The method is applied to the yeast Saccharomices Cerevisiae protein-protein interaction network. Robustness is tested in presence of a high percentage of unclassified proteins and under deletion/insertion of interactions.
Two processes can influence the evolution of protein interaction networks: addition and elimination of interactions between proteins, and gene duplications increasing the number of proteins and interactions. The rates of these processes can be estima
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help in the iden
From the spectral plot of the (normalized) graph Laplacian, the essential qualitative properties of a network can be simultaneously deduced. Given a class of empirical networks, reconstruction schemes for elucidating the evolutionary dynamics leading
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. Their identification is therefore necessary not only to understand complex formation but also
Motivation: High-throughput experimental techniques have been producing more and more protein-protein interaction (PPI) data. PPI network alignment greatly benefits the understanding of evolutionary relationship among species, helps identify conserve