Abstract
Network propagation is an important and widely used algorithm in systems biology, with applications in protein function prediction, disease gene prioritization, and patient stratification. However, up to this point it has required significant expertise to run. Here we extend the popular network analysis program Cytoscape to perform network propagation as an integrated function. Such integration greatly increases the access to network propagation by putting it in the hands of biologists and linking it to the many other types of network analysis and visualization available through Cytoscape. We demonstrate the power and utility of the algorithm by identifying mutations conferring resistance to Vemurafenib.
Highlights
Network propagation has become a critical analysis technique in computational systems biology
The basic network propagation process starts with some query nodes, and a network
The query nodes are given some initial value, a smoothing process is applied to the initial values on those query nodes, passing some of the value to neighboring nodes
Summary
Network propagation has become a critical analysis technique in computational systems biology. By examining the final distribution of values, we can, for instance, find a subnetwork where the nodes are closely related by the network to the original query. We introduce Diffusion, a network propagation algorithm delivered as both a new Cytoscape feature and as an internet service available to a broad array of web, desktop and server-based applications such as Jupyter notebooks.
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