Escher – a web application for visualizing data on biological pathways

We are now in the age of big data. More than ever before, biological discoveries require powerful and flexible tools for managing large datasets, including both visual and statistical tools. Pathway-based visualization is particularly powerful since it enables one to analyze complex datasets within the context of actual biological processes and to elucidate how each change in a cell effects related processes. To facilitate such approaches, researchers at UCSD have developed Escher, a web application that can be used to rapidly build pathway maps. On Escher maps, diverse datasets related to genes, reactions, and metabolites can be quickly contextualized within metabolism and, increasingly, beyond metabolism.

Three key features make Escher a uniquely effective tool for pathway visualization:

  1. Users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way.
  2. Users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)-in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).
  3. Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded.


Data visualization. A) The results of an in silico flux simulation visualized on the reactions. B) Metabolomics data for E. coli aerobic growth visualized on the metabolites. C) RNA-Seq data showing the shift from aerobic to anaerobic conditions in E. coli. Green represents reactions downregulated in anaerobic growth and red represents gene upregulated in anaerobic growth, based on the log2 of the fold change.

Availability – Escher is available now for free use (under the MIT license) at

King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO. (2015) Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PLoS Comput Biol 11(8):e1004321. [article]

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