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Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome.

ABSTRACT: The analysis of interaction networks is crucial for understanding molecular function and has an essential impact for genomewide studies. However, the interactomes of most species are largely incomplete and computational strategies that take into account sequence homology can help compensating for this lack of information using cross-species analysis. In this work we report the construction of a porcine interactome resource. We applied sequence homology matching and carried out bi-directional BLASTp searches for the currently available protein sequence collections of human and pig. Using this homology we were able to recover, on average, 71% of the proteins annotated for human pathways for the pig. Porcine protein-protein interactions were deduced from homologous proteins with known interactions in human. The result of this work is a resource comprising 204,699 predicted porcine interactions that can be used in genome analyses in order to enhance functional interpretation of data. The data can be visualized and downloaded from http://cpdb.molgen.mpg.de/pig.

SUBMITTER: Dreher F

PROVIDER: S-EPMC3273931 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome.

Dreher Felix F Kamburov Atanas A Herwig Ralf R

Evolutionary bioinformatics online 20120124

The analysis of interaction networks is crucial for understanding molecular function and has an essential impact for genomewide studies. However, the interactomes of most species are largely incomplete and computational strategies that take into account sequence homology can help compensating for this lack of information using cross-species analysis. In this work we report the construction of a porcine interactome resource. We applied sequence homology matching and carried out bi-directional BLA ...[more]

PMID: 22346341

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Project description:Optimizing the construction and update strategies for reference and candidate populations is the basis of the application of genomic selection (GS). In this study, we first simulated1200-purebred-pigs population that have been popular in China for 20 generations to study the effects of different population sizes and the relationship between individuals of the reference and candidate populations. The results showed that the accuracy was positively correlated with the size of the reference population within the same generation (r = 0.9366, p < 0.05), while was negatively correlated with the number of generation intervals between the reference and candidate populations (r = -0.9267, p < 0.01). When the reference population accumulated more than seven generations, the accuracy began to decline. We then simulated the population structure of 1200 purebred pigs for five generations and studied the effects of different heritabilities (0.1, 0.3, and 0.5), genotyping proportions (20, 30, and 50%), and sex ratios on the accuracy of the genomic estimate breeding value (GEBV) and genetic progress. The results showed that if the proportion of genotyping individuals accounts for 20% of the candidate population, the traits with different heritabilities can be genotyped according to the sex ratio of 1:1male to female. If the proportion is 30% and the traits are of low heritability (0.1), the sex ratio of 1:1 male to female is the best. If the traits are of medium or high heritability, the male-to-female ratio is 1:1, 1:2, or 2:1, which may achieve higher genetic progress. If the genotyping proportion is up to 50%, for low heritability traits (0.1), the proportion of sows from all genotyping individuals should not be less than 25%, and for the medium and high heritability traits, the optimal choice for the male-to-female ratio is 1:1, which may obtain the greatest genetic progress. This study provides a reference for determining a construction and update plan for the reference population of breeding pigs.

Dataset Information

Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome.

Publications

Construction of a pig physical interactome using sequence homology and a comprehensive reference human interactome.

Similar Datasets

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