Dataset Information

Phylogeny-guided interaction mapping in seven eukaryotes.

ABSTRACT:

Background

The assembly of reliable and complete protein-protein interaction (PPI) maps remains one of the significant challenges in systems biology. Computational methods which integrate and prioritize interaction data can greatly aid in approaching this goal.

Results

We developed a Bayesian inference framework which uses phylogenetic relationships to guide the integration of PPI evidence across multiple datasets and species, providing more accurate predictions. We apply our framework to reconcile seven eukaryotic interactomes: H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae and A. thaliana. Comprehensive GO-based quality assessment indicates a 5% to 44% score increase in predicted interactomes compared to the input data. Further support is provided by gold-standard MIPS, CYC2008 and HPRD datasets. We demonstrate the ability to recover known PPIs in well-characterized yeast and human complexes (26S proteasome, endosome and exosome) and suggest possible new partners interacting with the putative SWI/SNF chromatin remodeling complex in A. thaliana.

Conclusion

Our phylogeny-guided approach compares favorably to two standard methods for mapping PPIs across species. Detailed analysis of predictions in selected functional modules uncovers specific PPI profiles among homologous proteins, establishing interaction-based partitioning of protein families. Provided evidence also suggests that interactions within core complex subunits are in general more conserved and easier to transfer accurately to other organisms, than interactions between these subunits.

SUBMITTER: Dutkowski J

PROVIDER: S-EPMC2793266 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature

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Publications

Phylogeny-guided interaction mapping in seven eukaryotes.

Dutkowski Janusz J Tiuryn Jerzy J

BMC bioinformatics 20091130

<h4>Background</h4>The assembly of reliable and complete protein-protein interaction (PPI) maps remains one of the significant challenges in systems biology. Computational methods which integrate and prioritize interaction data can greatly aid in approaching this goal.<h4>Results</h4>We developed a Bayesian inference framework which uses phylogenetic relationships to guide the integration of PPI evidence across multiple datasets and species, providing more accurate predictions. We apply our fram ...[more]

PMID: 19948065

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Project description:To introduce a new skin dose mapping software system for interventional fluoroscopy dose assessment and to analyze the benefits and limitations of patient-phantom matching.In this study, a new software system was developed for visualizing patient skin dose during interventional fluoroscopy procedures. The system works by translating the reference point air kerma to the location of the patient's skin, which is represented by a computational model. In order to orient the model with the x-ray source, geometric parameters found within the radiation dose structured report (RDSR) are used along with a limited number of in-clinic measurements. The output of the system is a visual indication of skin dose mapped onto an anthropomorphic model at a resolution of 5 mm. In order to determine if patient-dependent and patient-sculpted models increase accuracy, peak skin dose was calculated for each of 26 patient-specific models and compared with doses calculated using an elliptical stylized model, a reference hybrid model, a matched patient-dependent model and one patient-sculpted model. Results were analyzed in terms of a percent difference using the doses calculated using the patient-specific model as the true standard.Anthropometric matching, including the use of both patient-dependent and patient-sculpted phantoms, was shown most beneficial for left lateral and anterior-posterior projections. In these cases, the percent difference using a reference model was between 8 and 20%, using a patient-dependent model between 7 and 15%, and using a patient-sculpted model between 3 and 7%. Under the table tube configurations produced errors less than 5% in most situations due to the flattening affects of the table and pad, and the fact that table height is the main determination of source-to-skin distance for these configurations. In addition to these results, several skin dose maps were produced and a prototype display system was placed on the in-clinic monitor of an interventional fluoroscopy system.The skin dose mapping program developed in this work represents a new tool that, as the RDSR becomes available through automated export or real-time streaming, can provide the interventional physician information needed to modify behavior when clinically appropriate. The program is nonproprietary and transferable, and also functions independent to the software systems already installed on the control room workstation. The next step will be clinical implementation where the workflow will be optimized along with further analysis of real-time capabilities.

Dataset Information

Phylogeny-guided interaction mapping in seven eukaryotes.

Background

Results

Conclusion

Publications

Phylogeny-guided interaction mapping in seven eukaryotes.

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