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F1000Res. 2014 Jul 1;3:141. doi: 10.12688/f1000research.4536.1. eCollection 2014.

Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results.

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1
The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.
2
The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.

Abstract

High-throughput OMICs experiments generate signals for millions of entities (i.e. genes, proteins, metabolites or any measurable biological entity) in the cell. In an effort to summarize and explore these signals, expression results are examined in the context of known pathways and processes, through enrichment analysis to generate a set of pathways and processes that is significantly enriched. Due to the high redundancy in annotation resources this often results in hundreds of sets. To facilitate the analysis of these results, we have developed the Enrichment Map app to visualize enrichments as a network. We have updated Enrichment Map to support Cytoscape 3, and have added additional features including new data formats and command line access.

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