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Issue 7, 2012
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C-GRAAL: Common-neighbors-based global GRAph ALignment of biological networks

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Abstract

Networks are an invaluable framework for modeling biological systems. Analyzing proteinprotein interaction (PPI) networks can provide insight into underlying cellular processes. It is expected that comparison and alignment of biological networks will have a similar impact on our understanding of evolution, biological function, and disease as did sequence comparison and alignment. Here, we introduce a novel pairwise global alignment algorithm called Common-neighbors based GRAph ALigner (C-GRAAL) that uses heuristics for maximizing the number of aligned edges between two networks and is based solely on network topology. As such, it can be applied to any type of network, such as social, transportation, or electrical networks. We apply C-GRAAL to align PPI networks of eukaryotic and prokaryotic species, as well as inter-species PPI networks, and we demonstrate that the resulting alignments expose large connected and functionally topologically aligned regions. We use the resulting alignments to transfer biological knowledge across species, successfully validating many of the predictions. Moreover, we show that C-GRAAL can be used to align human–pathogen inter-species PPI networks and that it can identify patterns of pathogen interactions with host proteins solely from network topology.

Graphical abstract: C-GRAAL: Common-neighbors-based global GRAph ALignment of biological networks

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Publication details

The article was received on 16 Oct 2011, accepted on 11 Dec 2011 and first published on 10 Jan 2012


Article type: Paper
DOI: 10.1039/C2IB00140C
Citation: Integr. Biol., 2012,4, 734-743
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    C-GRAAL: Common-neighbors-based global GRAph ALignment of biological networks

    V. Memišević and N. Pržulj, Integr. Biol., 2012, 4, 734
    DOI: 10.1039/C2IB00140C

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