Dataset Information

Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast.

ABSTRACT:

Background

In a genetic interaction, the phenotype of a double mutant differs from the combined phenotypes of the underlying single mutants. When the single mutants have no growth defect, but the double mutant is lethal or exhibits slow growth, the interaction is termed synthetic lethality or synthetic fitness. These genetic interactions reveal gene redundancy and compensating pathways. Recently available large-scale data sets of genetic interactions and protein interactions in Saccharomyces cerevisiae provide a unique opportunity to elucidate the topological structure of biological pathways and how genes function in these pathways.

Results

We have defined congruent genes as pairs of genes with similar sets of genetic interaction partners and constructed a genetic congruence network by linking congruent genes. By comparing path lengths in three types of networks (genetic interaction, genetic congruence, and protein interaction), we discovered that high genetic congruence not only exhibits correlation with direct protein interaction linkage but also exhibits commensurate distance with the protein interaction network. However, consistent distances were not observed between genetic and protein interaction networks. We also demonstrated that congruence and protein networks are enriched with motifs that indicate network transitivity, while the genetic network has both transitive (triangle) and intransitive (square) types of motifs. These results suggest that robustness of yeast cells to gene deletions is due in part to two complementary pathways (square motif) or three complementary pathways, any two of which are required for viability (triangle motif).

Conclusion

Genetic congruence is superior to genetic interaction in prediction of protein interactions and function associations. Genetically interacting pairs usually belong to parallel compensatory pathways, which can generate transitive motifs (any two of three pathways needed) or intransitive motifs (either of two pathways needed).

SUBMITTER: Ye P

PROVIDER: S-EPMC1310633 | biostudies-literature | 2005 Nov

REPOSITORIES: biostudies-literature

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Publications

Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast.

Ye Ping P Peyser Brian D BD Spencer Forrest A FA Bader Joel S JS

BMC bioinformatics 20051109

<h4>Background</h4>In a genetic interaction, the phenotype of a double mutant differs from the combined phenotypes of the underlying single mutants. When the single mutants have no growth defect, but the double mutant is lethal or exhibits slow growth, the interaction is termed synthetic lethality or synthetic fitness. These genetic interactions reveal gene redundancy and compensating pathways. Recently available large-scale data sets of genetic interactions and protein interactions in Saccharom ...[more]

PMID: 16283923

Similar Datasets

Project description:BackgroundAn important class of interaction switches for biological circuits and disease pathways are short binding motifs. However, the biological experiments to find these binding motifs are often laborious and expensive. With the availability of protein interaction data, novel binding motifs can be discovered computationally: by applying standard motif extracting algorithms on protein sequence sets each interacting with either a common protein or a protein group with similar properties. The underlying assumption is that proteins with common interacting partners will share some common binding motifs. Although novel binding motifs have been discovered with such approach, it is not applicable if a protein interacts with very few other proteins or when prior knowledge of protein group is not available or erroneous. Experimental noise in input interaction data can further deteriorate the dismal performance of such approaches.ResultsWe propose a novel approach of finding correlated short sequence motifs from protein-protein interaction data to effectively circumvent the above-mentioned limitations. Correlated motifs are those motifs that consistently co-occur only in pairs of interacting protein sequences, and could possibly interact with each other directly or indirectly to mediate interactions. We adopted the (l, d)-motif model and formulate finding the correlated motifs as an (l, d)-motif pair finding problem. We present both an exact algorithm, D-MOTIF, as well as its approximation algorithm, D-STAR to solve this problem. Evaluation on extensive simulated data showed that our approach not only eliminated the need for any prior protein grouping, but is also more robust in extracting motifs from noisy interaction data. Application on two biological datasets (SH3 interaction network and TGFbeta signaling network) demonstrates that the approach can extract correlated motifs that correspond to actual interacting subsequences.ConclusionThe correlated motif approach outlined in this paper is able to find correlated linear motifs from sparse and noisy interaction data. This, in turn, will expedite the discovery of novel linear binding motifs, and facilitate the studies of biological pathways mediated by them.

Dataset Information

Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast.

Background

Results

Conclusion

Publications

Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast.

Similar Datasets

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