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Activity Number: 413
Type: Contributed
Date/Time: Tuesday, August 5, 2014 : 2:00 PM to 3:50 PM
Sponsor: Section for Statistical Programmers and Analysts
Abstract #313691
Title: Redundancy Control in Pathway Databases (RECIPA): An Open-Source Application for Improving Pathway Analysis of Large Genomic and Genetic Data Sets
Author(s): Juan Vivar*+
Companies: BBRI - NCCU
Keywords: Pathway analysis ; Redundancies ; Databases
Abstract:

Pathway analysis is a powerful approach for interrogating large genomic and genetic data leading to the identification of biological mechanisms associated with outcomes of interest. While several factors can influence the outcome, the dependence of the obtained results on the content of pathway databases is an important but underexplored area of study. Pathway databases often contain differently named pathways that overlap with one another to varying degrees, leading to redundancies among them. Ignoring these could lead to the designation of pathways as being significant and highly ranked due to high content-similarity, rather than truly independent biological mechanisms. Statistically, such dependencies can result in correlated p-values and overdispersion, leading to biased results. This study represents one of the first attempts at characterizing content-redundancy in pathway databases and its effects on pathway analysis. We provide an application in R, ReCiPa (Redundancy Control in Pathway Databases), which enables the end-user to control overlap in pathway databases. ReCiPa is expected to result in notable improvements in pathway analysis outputs from genomic and genetic data.


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