Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs".

By Lisa Matthews, P. Vaglio, J. Reboul, Hui Ge, B. Davis, J. Garrels, S. Vincent, Marc Vidal. 2001

500 citations recorded by the source corpus.

Protein interaction maps have provided insight into the relationships among the predicted proteins of model organisms for which a genome sequence is available. These maps have been useful in generating potential interaction networks, which have confirmed the existence of known complexes and pathways and have suggested the existence of new complexes and or crosstalk between previously unlinked pathways. However, the generation of such maps is costly and labor intensive. Here, we investigate the extent to which a protein interaction map generated in one species can be used to predict interactions in another species.

Subfields: Molecular Biology

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Citations in the corpus

SWISS-MODEL: homology modelling of protein structures and complexes (2018, positive): “Similar to comparative modelling of monomeric proteins, the information of a protein’s quaternary structure is transferred by homology to another one, and a model of the complex is obtained based on the structures of the interacting homologs, i.e. in-terologs, as templates (19–21).”
Similarities and Differences in Genome-Wide Expression Data of Six Organisms (2003, result): “The potential of including functional genomic properties in a comparison analysis was demonstrated in recent studies that compared protein– protein interaction networks of different organisms (Matthews et al. 2001; Kelley et al. 2003).”
Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases (2007, background): “Sequence-based searches for ‘‘interologs’’ were able to identify 16%–31% of true ‘‘interologs’’ (tested using Y2H system) even between remotely related species such as yeast and worm [96].”
IsoRankN: spectral methods for global alignment of multiple protein networks (2009, background): “Aproblem with accurate cross-species comparison of such networks is that the known networks, however, are both incomplete and inaccurate (Han et al ., 2005; Huang et al ., The speciﬁc problem we address is that of global alignment of multiple PPI networks.”
Empirically-controlled mapping of the Caenorhabditis elegans protein-protein interactome network (2009, background): “…to a speciﬁc biological process 1,6–11 , ‘interolog’ interactions—that is, predicted pairs of interactors whose respective orthologs interact in another organism 12 —and lastly, Y2H interactions derived from a high-throughput screen performed with B 2,000 metazoan proteins as baits 3 (WI-2004).”
A human protein-protein interaction network: a resource for annotating the proteome. (2005, unknown): “In addition, bioinformatic analyses have been performed, collecting information on human interactions from hypothesis-driven studies (Peri et al., 2003) or from studies identifying conserved orthologous interactions (Lehner and Fraser, 2004), which are referred to as “interologs” ( Matthews et al., ”
FlyMine: an integrated database for Drosophila and Anopheles genomics (2007, background): “For example, identification of so-called interologues (putative interacting protein pairs whose orthologues in another organism also apparently interact), can add confidence to interactions [13].”
Integrative approaches for finding modular structure in biological networks (2013, background): “…to identifying conservation at the network level, individual interactions have been observed to occur between orthologous gene pairs in two species, corresponding to conserved protein–protein interactions (known as interologues) 111 or conserved regulatory interactions (known as regulogues) 112 .”
Differential network biology (2012, background): “For example, the PPI networks of Saccharomyces cerevisiae were compared against other microbial species such as Helicobacter pylori to predict previously uncharacterized PPIs (Matthews et al , 2001; Yu et al , 2004) or to identify evolutionarily conserved protein complexes (Kelley et al , 2003).”
Online Predicted Human Interaction Database (2005, unknown): “Homology-based approaches to predicting PPIs may contain some inaccuracies (Deane et al. , 2002; Matthews et al. , 2001) depending on the filtering criteria used.”