Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions

Evolutionary bioinformatics online, 2007

13,439 citations recorded by the source corpus.

Motivation: Although a great deal of progress is being made in the development of fast and reliable experimental techniques to extract genome-wide networks of protein-protein and protein-DNA interactions, the sequencing of new genomes proceeds at an even faster rate. That is why there is a considerable need for reliable methods of in-silico prediction of protein interaction based solely on sequence similarity information and known interactions from well-studied organisms. This problem can be solved if a dependency exists between sequence similarity and the conservation of the proteins’ functions. Results: In this paper, we introduce a novel probabilistic method for prediction of protein-protein interactions using a new empirical probabilistic formula describing the loss of interactions between homologous proteins during the course of evolution. This formula describes an evolutional process quite similar to the process of the Earth’s population growth. In addition, our method favors predictions confirmed by several interacting pairs over predictions coming from a single interacting pair. Our approach is useful in working with “noisy” data such as those coming from high-throughput experiments. We have generated predictions for five “model” organisms: H. sapiens, D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae and evaluated the quality of these predictions.

View Paper: https://www.semanticscholar.org/paper/47e675f4a694d81a1605e6706b30825ace2b324f

Citations in the corpus

• Phylogeography and conservation of the bull shark (Carcharhinus leucas) inferred from mitochondrial and microsatellite DNA (2011, methodology): “The number and frequency of haplotypes, polymorphic sites, and transition and transversions were calculated using ARLEQUIN version 3.11 (Excoffier et al. 2005).”
• Vicariance patterns in the Mediterranean Sea: east–west cleavage and low dispersal in the endemic seagrass Posidonia oceanica (2007, methodology): “The hierarchical structure of genetic variation at the whole Mediterranean scale was examined using arlequin software (Excoffier et al., 2005).”
• Refugia within refugia: the case study of a canopy tree (Eurycorymbus cavaleriei) in subtropical China (2009, background): “3.01 (Excoffier et al., 2005): number of haplotypes, gene diversity (h) and nucleotide diversity (p).”
• Genetic variability of the Amazon River prawn Macrobrachium amazonicum (Decapoda, Caridea, Palaemonidae) (2011, result): “with a previous phylogenetic analysis of Macrobrachium (Pileggi and Mantelatto, 2010), in which M. acanthurus and M. jelskii appear as related taxa. A morphologically based analysis by Pileggi (2009) indicated that M.”
• After continents divide: comparative phylogeography of reef fishes from the Red Sea and Indian Ocean (2013, methodology): “ª 2013 Blackwell Publishing Ltd 3 Genetic diversity and population structure Arlequin 3.5 (Excoffier et al., 2005) was used to calculate haplotype and nucleotide diversity (h and p, respectively), and to test for population structure among sampling sites for each species and molecular marker (i.e.…”
• High gene flow in oceanic bottlenose dolphins (Tursiops truncatus) of the North Atlantic (2007, unknown): “These calculations were performed with Arlequin 3.1 (Excoffier et al. 2005).”
• Phylogeography of the chestnut‐tailed antbird (Myrmeciza hemimelaena) clarifies the role of rivers in Amazonian biogeography (2012, methodology): “1 (Excoffier et al., 2005): nucleotide diversity (p), haplotype diversity (h), and Tajima’s D (Tajima, 1989) and”
• Evolutionary pathways among shallow and deep-sea echinoids of the genus Sterechinus in the Southern Ocean (2011, methodology): “In addition, we calculated the pairwise genetic p-distances between pairs of morphospecies with the program Arlequin 3.1 (Excoffier et al., 2005).”
• Contrasting phylogeographical patterns for springtails reflect different evolutionary histories between the Antarctic Peninsula and continental Antarctica (2009, methodology): “arlequin version 3.11 (Excoffier et al., 2005) was used to explore the genetic characteristics of populations and to test for the presence of population structure for each species separately.”