Exploiting indirect neighbours and topological weight to predict protein function from protein-protein interactions
Hon Nian Chua,Wing-Kin Sung,Limsoon Wong +2 more
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TLDR
An algorithm is developed that predicts the functions of a protein in two steps: assigning a weight to each of its level-1 and level-2 neighbours by estimating its functional similarity with the protein using the local topology of the interaction network as well as the reliability of experimental sources and scoring each function based on its weighted frequency in these neighbours.Abstract:
Most approaches in predicting protein function from protein-protein interaction data utilize the observation that a protein often share functions with proteins that interacts with it (its level-1 neighbours). However, proteins that interact with the same proteins (i.e. level-2 neighbours) may also have a greater likelihood of sharing similar physical or biochemical characteristics. We speculate that two separate forms of functional association accounts for such a phenomenon, and a protein is likely to share functions with its level-1 and/or level-2 neighbours. We are interested to find out how significant is functional association between level-2 neighbours and how they can be exploited for protein function prediction.
We made a statistical study on recent interaction data and observed that functional association between level-2 neighbours is clearly observable. A substantial number of proteins are observed to share functions with level-2 neighbours but not with level-1 neighbours. We develop an algorithm that predicts the functions of a protein in two steps: (1) assign a weight to each of its level-1 and level-2 neighbours by estimating its functional similarity with the protein using the local topology of the interaction network as well as the reliability of experimental sources; (2) scoring each function based on its weighted frequency in these neighbours. Using leave-one-out cross validation, we compare the performance of our method against that of several other existing approaches and show that our method performs well.read more
Citations
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Network-based prediction of protein function
TL;DR: The current computational approaches for theFunctional annotation of proteins are described, including direct methods, which propagate functional information through the network, and module‐assisted methods, who infer functional modules within the network and use those for the annotation task.
Journal ArticleDOI
A Survey of Link Prediction in Complex Networks
TL;DR: This survey will review the general-purpose techniques at the heart of the link prediction problem, which can be complemented by domain-specific heuristic methods in practice.
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Complex discovery from weighted PPI networks
TL;DR: An algorithm called CMC (clustering-based on maximal cliques) is developed to discover complexes from the weighted PPI network and is shown to be an effective approach to protein complex prediction from protein interaction network.
Journal ArticleDOI
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins.
Pingzhao Hu,Sarath Chandra Janga,Sarath Chandra Janga,Mohan Babu,J. Javier Díaz-Mejía,J. Javier Díaz-Mejía,Gareth Butland,Wenhong Yang,Oxana Pogoutse,Xinghua Guo,Sadhna Phanse,Peter D Wong,Shamanta Chandran,Constantine C. Christopoulos,Anaies Nazarians-Armavil,Negin Karimi Nasseri,Gabriel Musso,Mehrab Ali,Nazila Nazemof,Veronika Eroukova,Ashkan Golshani,Alberto Paccanaro,Jack Greenblatt,Gabriel Moreno-Hagelsieb,Andrew Emili +24 more
TL;DR: An extensive proteomic survey using affinity-tagged E. coli strains is performed and comprehensive genomic context inferences are generated to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel.
Journal ArticleDOI
From link-prediction in brain connectomes and protein interactomes to the local-community-paradigm in complex networks
Carlo Vittorio Cannistraci,Gregorio Alanis-Lobato,Gregorio Alanis-Lobato,Timothy Ravasi,Timothy Ravasi +4 more
TL;DR: It is shown how a link/community-based strategy triggers substantial prediction improvements because it accounts for the singular topology of several real networks organised in multiple local communities - a tendency here named local-community-paradigm (LCP).
References
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The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
Andreas Ruepp,Alfred Zollner,Dieter Maier,Kaj Albermann,Jean Hani,Martin Mokrejs,Igor V. Tetko,Ulrich Güldener,Gertrud Mannhaupt,Martin Münsterkötter,H. Werner Mewes +10 more
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Book
Network-based prediction of protein function
TL;DR: The current computational approaches for theFunctional annotation of proteins are described, including direct methods, which propagate functional information through the network, and module‐assisted methods, who infer functional modules within the network and use those for the annotation task.
Posted Content
Global protein function prediction in protein-protein interaction networks
TL;DR: In this article, the authors propose to assign functional classes to proteins from their network of physical interactions, by minimizing the number of interacting proteins with different categories, based on the entire connectivity pattern of the protein network.
Journal ArticleDOI
A Survey of Link Prediction in Complex Networks
TL;DR: This survey will review the general-purpose techniques at the heart of the link prediction problem, which can be complemented by domain-specific heuristic methods in practice.