PPubMed31 Aug 2010Cited 60×

Finding the Right Questions: Exploratory Pathway Analysis to Enhance Biological Discovery in Large Datasets

Thomas Kelder, Bruce R. Conklin, Chris T. Evelo, Alexander R. Pico, Jonathan A. Eisen

Abstract

'Jonathan A. Eisen'] This Essay discusses the role of pathways for exploratory data analysis in present-day biology.

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Pathway diagrams are powerful visual tools that can guide exploratory data analysis, but current tools lack flexibility, interactivity, and integration.

What’s new

i.Highlights the role of pathway diagrams in exploratory data analysis.
ii.Identifies three key properties—flexibility, interactivity, effectiveness—needed for exploratory pathway tools.
iii.Reviews existing pathway visualization tools and standards, pointing out gaps.
iv.Proposes design guidelines (e.g., APIs, semantic zooming) for future tool development.

How they did it

The authors review the literature on exploratory data analysis and pathway visualization, compare existing tools and standards, and synthesize design principles for more effective exploratory pathway analysis. They illustrate concepts with examples such as metabolic pathway mapping and discuss challenges and opportunities for developers.

Caveats

✕Current pathway analysis tools are isolated and hard to combine.
✕Lack of a comprehensive framework for exploration and visualization limits their utility.
✕Mapping data to different identifier systems and reformatting datasets remain cumbersome.
✕Visualizing all possible interactions can create incomprehensible “hairball” networks.

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