title: Unlocking proteomic heterogeneity in complex diseases through visual analytics.
abstract: Despite years of preclinical development, biological interventions designed to treat complex diseases such as asthma often fail in phase III clinical trials. These failures suggest that current methods to analyze biomedical data might be missing critical aspects of biological complexity such as the assumption that cases and controls come from homogeneous distributions. Here we discuss why and how methods from the rapidly evolving field of visual analytics can help translational teams (consisting of biologists, clinicians, and bioinformaticians) to address the challenge of modeling and inferring heterogeneity in the proteomic and phenotypic profiles of patients with complex diseases. Because a primary goal of visual analytics is to amplify the cognitive capacities of humans for detecting patterns in complex data, we begin with an overview of the cognitive foundations for the field of visual analytics. Next, we organize the primary ways in which a specific form of visual analytics called networks has been used to model and infer biological mechanisms, which help to identify the properties of networks that are particularly useful for the discovery and analysis of proteomic heterogeneity in complex diseases. We describe one such approach called subject-protein networks, and demonstrate its application on two proteomic datasets. This demonstration provides insights to help translational teams overcome theoretical, practical, and pedagogical hurdles for the widespread use of subject-protein networks for analyzing molecular heterogeneities, with the translational goal of designing biomarker-based clinical trials, and accelerating the development of personalized approaches to medicine.
authors: Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA.
authors: Suresh K
authors: SK
authors: Bhavnani
authors: Bryant
authors: B
authors: Dang
authors: Gowtham
authors: G
authors: Bellala
authors: Rohit
authors: R
authors: Divekar
authors: Shyam
authors: S
authors: Visweswaran
authors: Allan R
authors: AR
authors: Brasier
authors: Alex
authors: A
authors: Kurosky
mesh_terms: D001907:Boutonneuse Fever / Q000378:metabolism; D003196:Computer Graphics; D003627:Data Interpretation, Statistical; D053263:Gene Regulatory Networks; D006801:Humans; D060066:Protein Interaction Maps; D020543:Proteome / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods
chemical_list: D020543:Proteome
keywords: Bioinformatics; Molecular and clinical profiles; Network analysis; Personalized medicine; Proteomic heterogeneity; Subject-Protein Networks