BackgroundMolecular and systems biologists are tasked with the comprehension and analysis of incredibly complex networks of biochemical interactions, called pathways, that occur within a cell. Through interviews with domain experts, we identified four common tasks that require an understanding of the causality within pathways, that is, the downstream and upstream relationships between proteins and biochemical reactions, including: visualizing downstream consequences of perturbing a protein; finding the shortest path between two proteins; detecting feedback loops within the pathway; and identifying common downstream elements from two or more proteins.ResultsWe introduce ReactionFlow, a visual analytics application for pathway analysis that emphasizes the structural and causal relationships amongst proteins, complexes, and biochemical reactions within a given pathway. To support the identified causality analysis tasks, user interactions allow an analyst to filter, cluster, and select pathway components across linked views. Animation is used to highlight the flow of activity through a pathway.ConclusionsWe evaluated ReactionFlow by providing our application to two domain experts who have significant experience with biomolecular pathways, after which we conducted a series of in-depth interviews focused on each of the four causality analysis tasks. Their feedback leads us to believe that our techniques could be useful to researchers who must be able to understand and analyze the complex nature of biological pathways. ReactionFlow is available at https://github.com/CreativeCodingLab/ReactionFlow.
An essential element of exploratory data analysis is the use of revealing low-dimensional projections of high-dimensional data. Projection Pursuit has been an effective method for finding interesting low-dimensional projections of multidimensional spaces by optimizing a score function called a projection pursuit index. However, the technique is not scalable to high-dimensional spaces. Here, we introduce a novel method for discovering noteworthy views of high-dimensional data spaces by using binning and random projections. We define score functions, akin to projection pursuit indices, that characterize visual patterns of the low-dimensional projections that constitute feature subspaces. We also describe an analytic, multivariate visualization platform based on this algorithm that is scalable to extremely large problems.
In this paper we introduce TimeArcs, a novel visualization technique for representing dynamic relationships between entities in a network. Force-directed layouts provide a way to highlight related entities by positioning them near to each other. Entities are brought closer to each other (forming clusters) by forces applied on nodes and connections between nodes. In many application domains, relationships between entities are not temporally stable, which means that cluster structures and cluster memberships also may vary across time. Our approach merges multiple force-directed layouts at different time points into a single comprehensive visualization that provides a big picture overview of the most significant clusters within a user-defined period of time. TimeArcs also supports a range of interactive features, such as allowing users to drill-down in order to see details about a particular cluster. To highlight the benefits of this technique, we demonstrate its application to various datasets, including the IMDB co-star network, a dataset showing conflicting evidences within biomedical literature of protein interactions, and collocated popular phrases obtained from political blogs.
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