title: Visual integration of quantitative proteomic data, pathways, and protein interactions.
abstract: We introduce several novel visualization and interaction paradigms for visual analysis of published protein-protein interaction networks, canonical signaling pathway models, and quantitative proteomic data. We evaluate them anecdotally with domain scientists to demonstrate their ability to accelerate the proteomic analysis process. Our results suggest that structuring protein interaction networks around canonical signaling pathway models, exploring pathways globally and locally at the same time, and driving the analysis primarily by the experimental data, all accelerate the understanding of protein pathways. Concrete proteomic discoveries within T-cells, mast cells, and the insulin signaling pathway validate the findings. The aim of the paper is to introduce novel protein network visualization paradigms and anecdotally assess the opportunity of incorporating them into established proteomic applications. We also make available a prototype implementation of our methods, to be used and evaluated by the proteomic community.
authors.affiliation: Department of Computer Sciences, Brown University, Providence, RI 02912, USA. jr@cs.brown.edu
authors.forename: Radu
authors.initials: R
authors.lastname: Jianu
authors.forename: Kebing
authors.initials: K
authors.lastname: Yu
authors.forename: Lulu
authors.initials: L
authors.lastname: Cao
authors.forename: Vinh
authors.initials: V
authors.lastname: Nguyen
authors.forename: Arthur R
authors.initials: AR
authors.lastname: Salomon
authors.forename: David H
authors.initials: DH
authors.lastname: Laidlaw
mesh_terms: D003196:Computer Graphics; D003198:Computer Simulation; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D018511:Systems Integration; D014584:User-Computer Interface
chemical_list: D020543:Proteome
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