Analysis and correction of crosstalk effects in pathway analysis
- Michele Donato1,
- Zhonghui Xu2,
- Alin Tomoiaga3,
- James G Granneman1,
- Robert G Mackenzie1,
- Riyue Bao1,
- Nandor Gabor Than1,
- Peter H Westfall3,
- Roberto Romero2 and
- Sorin Draghici1,4
- ↵* Corresponding author; email: sorin{at}wayne.edu
Abstract
Identifying the pathways that are significantly impacted in a given condition is a crucial step in understanding the underlying biological phenomena. All approaches currently available for this purpose calculate a p-value that aims to quantify the significance of the involvement of each pathway in the given phenotype. These p-values were previously thought to be independent. Here we show that this is not the case, and that many pathways can considerably affect each other's p-values through a "crosstalk" phenomenon. Although it is intuitive that various pathways could influence each other, the presence and extent of this phenomenon have not been rigorously studied and, most importantly, there is no currently available technique able to quantify the amount of such crosstalk. Here, we show that all three major categories of pathway analysis methods (enrichment analysis, functional class scoring, and topology-based methods) are severely influenced by crosstalk phenomena. Using real pathways and data, we show that in some cases pathways with significant p-values are not biologically meaningful, and that some biologically meaningful pathways with non-significant p-values become statistically significant when the crosstalk effects of other pathways are removed. We describe a technique able to detect, quantify, and correct crosstalk effects, as well as identify independent functional modules. We assessed this novel approach on data from four real experiments coming from three phenotypes involving two species. This method is expected to allow a better understanding of individual experiment results, as well as a more refined definition of the existing signaling pathways for specific phenotypes.
- Received December 12, 2012.
- Accepted August 6, 2013.
- © 2013, Published by Cold Spring Harbor Laboratory Press
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