EPA Science Inventory

Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes

Citation:

Williams-DeVane, C., D. Reif, E. Hubal, P. Bushel, E. Hudgens, J. Gallagher, AND S. Edwards. Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes. BMC Systems Biology. BioMed Central Ltd, London, Uk, 7(1):119, (2013).

Description:

Complex diseases are often difficult to diagnose, treat, and study due to the multi-factorial nature of the etiology. Significant challenges exist with regard to how to segregate indivdiuals into suitable subtypes of the disease. Here, we examine a range of methods for evaluating gene expression and clinical indicators of allergy and childhood asthma to inform the basic mechanistic underpinnings of disease etiology. We compared traditional methods such as Student's t-test and single data domain clustering as well as more complex, multi-data domain methods such as multi-step decision tree and modk-prototypes algorithm analysis strategies to determine the best method to segregate asthmatics. Traditional methods did not segregate asthmatics and non-asthmatics well, were difficult to interpret and provided sparse mechanistic insight. Methods that incorporate multiple domains of data performed better overall. The understanding gained from the use of this case study will lead to better understanding of complex disease in general by comparison and application of more efficient methodologies.

Purpose/Objective:

The understanding gained from the use of this case study will lead to better understanding of complex disease in general by comparison and application of more efficient methodologies.

URLs/Downloads:

WILLIAMS-DEVANE-ORD-000442.PDF   (PDF,NA pp, 184.043 KB,  about PDF)

Record Details:

Record Type: DOCUMENT (JOURNAL/PEER REVIEWED JOURNAL)
Start Date: 03/26/2014
Completion Date: 03/26/2014
Record Last Revised: 07/28/2014
Record Created: 03/26/2014
Record Released: 03/26/2014
OMB Category: Other
Record ID: 271872

Organization:

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF RESEARCH AND DEVELOPMENT

NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS RESEARCH LAB

INTEGRATED SYSTEMS TOXICOLOGY DIVISION