Monday, March 4, 2013

COMPLEAT complex enrichment tool

The DRSC is pleased to announce that we are making COMPLEAT available in our suite of online software tools.

Conceptually similar to gene set enrichment, COMPLEAT makes it possible to look for enrichment of predicted protein complexes in a large-scale RNAi data set--including those with multiple conditions or time-points. You'll see a graph (left-hand side) and can click do draw a polygon around points on the graph to view those specific complexes (right-hand side).

The online tool web pages include a Demo (narrated video) and a set of Example Files so you can test out the tool and see the data upload format. As always, your feedback is welcome!

Here's the citation and abstract from the paper, as well as a screenshot.

Vinayagam A, Hu Y, Kulkarni M, Roesel C, Sopko R, Mohr SE, Perrimon N. Protein complex-based analysis framework for high-throughput data sets.  Sci Signal. 2013 Feb 26;6(264):rs5. PMID: 23443684

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 (, 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.

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