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

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.

Cited by papers we hold 3

• Integrated analysis of single-cell embryo data yields a unified transcriptome signature for the human preimplantation epiblast · 2018
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• Post-mortem molecular profiling of three psychiatric disorders · 2017
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• Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer · 2016
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