Multiple testing tool to detect combinatorial effects in biology

Abstract

Detecting combinatorial effects is important to various research areas, including biology, genomics, and medical sciences. However, this task was not only computationally nontrivial but also extremely difficult to achieve because of the necessity of a multiple testing procedure; hence few methods can comprehensively analyze high-order combinations. Recently, Limitless Arity Multiple-testing Procedure (LAMP) was introduced, allowing us to enumerate statistically significant combinations from a given dataset. This chapter provides instructions for LAMP using simple examples of combinatorial transcription factor regulation discovery and visualization of the results. This chapter also introduces LAMPLINK, which is extended software of LAMP. LAMPLINK can handle genetic dataset to detect statistically significant interactions among multiple SNPs from a genome-wide association study (GWAS) dataset.