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. 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

Ruth Isserlin  1 , Daniele Merico  2 , Veronique Voisin  1 , Gary D Bader  1
Affiliations

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

Ruth Isserlin et al. F1000Res. .

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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Conflict of interest statement

Competing interests: No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Enrichment Map app user interface
Illustration of Enrichment Map user interface which consists of four main parts: analysis type, file specifications, node and edge filtering. For each analysis type there is a different set of required files. For added functionality there are a set of optional files that can be included to help annotate and explore results. Tuning parameters such as p-value and q-value helps control the number of nodes while tuning the similarity coefficient helps control the number of edges.
Figure 2.
Figure 2.. Enrichment Map build process overview.
Figure 3.
Figure 3.. Enrichment Map of heart fibroblast versus tail fibroblast expression.
Using the search field you can enter any text to search all attributes of the given network. Highlighted nodes, (shown as yellow nodes with red edges just left of center) are genesets that contain the gene TBX20.
Figure 4.
Figure 4.. Node Heat Map Panel (contained in the Cytoscape table panel) displayed on selection of “Pericardium development (GO:0060039)” gene set.
If GSEA results are loaded into Enrichment Map, GSEA leading edge genes, defined as the set of genes that contribute most to the enrichment, are highlighted in yellow.
See this image and copyright information in PMC

References

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