Reference: Vinayagam A, et al. (2013) Protein complex-based analysis framework for high-throughput data sets. Sci Signal 6(264):rs5

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Abstract


Analysis of high-throughput data increasingly relies on pathway annotation and functional information derived from Gene Ontology. This approach has limitations, in particular for the analysis of network dynamics over time or under different experimental conditions, in which modules within a network rather than complete pathways might respond and change. We report an analysis framework based on protein complexes, which are at the core of network reorganization. We generated a protein complex resource for human, Drosophila, and yeast from the literature and databases of protein-protein interaction networks, with each species having thousands of complexes. We developed COMPLEAT (http://www.flyrnai.org/compleat), a tool for data mining and visualization for complex-based analysis of high-throughput data sets, as well as analysis and integration of heterogeneous proteomics and gene expression data sets. With COMPLEAT, we identified dynamically regulated protein complexes among genome-wide RNA interference data sets that used the abundance of phosphorylated extracellular signal-regulated kinase in cells stimulated with either insulin or epidermal growth factor as the output. The analysis predicted that the Brahma complex participated in the insulin response.

Reference Type
Journal Article | Research Support, N.I.H., Extramural | Research Support, Non-U.S. Gov't | Validation Study
Authors
Vinayagam A, Hu Y, Kulkarni M, Roesel C, Sopko R, Mohr SE, Perrimon N
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Gene Ontology Annotations


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Gene/Complex Qualifier Gene Ontology Term Aspect Annotation Extension Evidence Method Source Assigned On Reference

Phenotype Annotations


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Gene Phenotype Experiment Type Mutant Information Strain Background Chemical Details Reference

Disease Annotations


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Gene Disease Ontology Term Qualifier Evidence Method Source Assigned On Reference

Regulation Annotations


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Regulator Target Direction Regulation Of Happens During Method Evidence

Post-translational Modifications


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Site Modification Modifier Reference

Interaction Annotations


Genetic Interactions

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Interactor Interactor Allele Assay Annotation Action Phenotype SGA score P-value Source Reference

Physical Interactions

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Interactor Interactor Assay Annotation Action Modification Source Reference

Functional Complementation Annotations


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Gene Species Gene ID Strain background Direction Details Source Reference