Entourage: Visualizing Relationships between Biological Pathways using Contextual Subsets

Abstract

Biological pathway maps are highly relevant tools for many tasks in molecular biology. They reduce the complexity of the overall biological network by partitioning it into smaller manageable parts. While this reduction of complexity is their biggest strength, it is, at the same time, their biggest weakness. By removing what is deemed not important for the primary function of the pathway, biologists lose the ability to follow and understand cross-talks between pathways. Considering these cross-talks is, however, critical in many analysis scenarios, such as judging effects of drugs. In this paper we introduce Entourage, a novel visualization technique that provides contextual information lost due to the artificial partitioning of the biological network, but at the same time limits the presented information to what is relevant to the analyst's task. We use one pathway map as the focus of an analysis and allow a larger set of contextual pathways. For these context pathways we only show the contextual subsets, i.e., the parts of the graph that are relevant to a selection. Entourage suggests related pathways based on similarities and highlights parts of a pathway that are interesting in terms of mapped experimental data. We visualize interdependencies between pathways using stubs of visual links, which we found effective yet not obtrusive. By combining this approach with visualization of experimental data, we can provide domain experts with a highly valuable tool. We demonstrate the utility of Entourage with case studies conducted with a biochemist who researches the effects of drugs on pathways. We show that the technique is well suited to investigate interdependencies between pathways and to analyze, understand, and predict the effect that drugs have on different cell types.

Visual Analysis of Relationships between Heterogeneous Networks and Texts: An Application on the IEEE VIS Publication Dataset

“…Caleydo [4], for instance, shows networks side by side in a 2.5D environment. Entourage [5] uses a focus+context approach to explore relationships in biological pathways. While analysts explore a pathway and focus on specific nodes, parts of related pathways are shown in additional views as contextual subsets.…”

“…For instance, some metabolic networks from the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database [33] have a precomputed layout, which is preferred by biologists, but the networks are still connected with each other. In this case, it would be beneficial to have multiple views on the networks and provide a means to navigate the relationships, similar to the approach facilitated by Entourage [5]. In another scenario, multiple networks could be merged into one single network view.…”

Scalable graph exploration and visualization: Sensemaking challenges and opportunities

“…Filtering [1], [2], [3] Sampling [4], [5], [6] Partitioning [7], [8], [9], [10] Clustering [11], [12], [13], [3], [14], [15] Local View Free Discovery Exploration [16], [17], [14], [18], [3], [15], [19], [20], [21] Network Motifs [22], [23], [24], [25], [26] Targeted Discovery Pattern Matching [27], [28], [29], [30], [31] Navigation [32], [33], [34], [35], [36], [19], [37] Fig. 1.…”

“…The system Entourage, a tool for visualizing biological pathways, uses contextual information provided by the user to visualize interdependencies among pathways [20]. Once a subset of a pathway has been selected, other pathways sharing that subset (or elements from it) are displayed, ranked by their similarity.…”

NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity

“…To reduce the amount of visual clutter, we draw visual links (i.e., synaptic connections) between neurites only ondemand, when hovering over a synapse (S5-scalable to many connections between neurites). Displaying stubs instead of lines [27] would be a viable alternative to reduce clutter while still indicating connections. However, in our case a synapse node on a neurite already indicates the presence of a connection.…”