Epistasis Blog

From the Computational Genetics Laboratory at the University of Pennsylvania (www.epistasis.org)

Monday, January 11, 2016

An integrated network approach to identifying biological pathways and environmental exposures associated with complex diseases

Our paper from 2016 Pacific Symposium on Biocomputing (PSB)

Darabos C, Qiu J, Moore JH. An integrated network approach to identifying biological pathways and environmental exposure interactions in complex diseases. Pac Symp Biocomput. 2016;21:9-20. [PDF]


Abstract


Complex diseases are the result of intricate interactions between genetic, epigenetic and environmental factors. In previous studies, we used epidemiological and genetic data linking environmental exposure or genetic variants to phenotypic disease to construct Human Phenotype Networks and separately analyze the effects of both environment and genetic factors on disease interactions. To better capture the intricacies of the interactions between environmental exposure and the biological pathways in complex disorders, we integrate both aspects into a single "tripartite" network. Despite extensive research, the mechanisms by which chemical agents disrupt biological pathways are still poorly understood. In this study, we use our integrated network model to identify specific biological pathway candidates possibly disrupted by environmental agents. We conjecture that a higher number of co-occurrences between an environmental substance and biological pathway pair can be associated with a higher likelihood that the substance is involved in disrupting that pathway. We validate our model by demonstrating its ability to detect known arsenic and signal transduction pathway interactions and speculate on candidate cell-cell junction organization pathways disrupted by cadmium. The validation was supported by distinct publications of cell biology and genetic studies that associated environmental exposure to pathway disruption. The integrated network approach is a novel method for detecting the biological effects of environmental exposures. A better understanding of the molecular processes associated with specific environmental exposures will help in developing targeted molecular therapies for patients who have been exposed to the toxicity of environmental chemicals.

Tuesday, January 05, 2016

A call for biological data mining approaches in epidemiology

Our open-access editorial in BioData Mining on the need for data mining and machine learning in epidemiology.

Lynch SM, Moore JH. A call for biological data mining approaches in epidemiology. BioData Min. 2016 Jan 4;9:1. [PDF]