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More than three transcription factors often work together to enable cells to respond to various signals. The detection of combinatorial regulation by multiple transcription factors, however, is not only computationally nontrivial but also extremely unlikely because of multiple testing correction. The exponential growth in the number of tests forces us to(More)
—Three or more transcription factors (TFs) often work together, and the combinatorial regulations are essential in cellular machinery. However, it is impossible to discover statistically significant sets of TF binding motifs due to the necessity of the multiple testing procedure. To improve the sensitivity of widely used Bonferroni correction or its(More)
(Abstract) In many scientific communities using experiment databases, one of the crucial problem is how to assess the statistical significance (P-value) of a discovered hypothesis. Especially, combinatorial hypothesis assessment is a hard problem because it requires a multiple-testing procedure with a very large factor of the P-value correction. Recently,(More)
A gene network is constructed with genes as nodes, and interactions between genes as edges so as to reveal unknown gene functions and relationship. However, nodes and edges of gene networks are usually very numerous. Because of that, it may be difficult to understand relations between genomic functions and gene-gene interactions, if it is visualized by(More)
The habitats of polyploid species are generally distinct from their parental species. Stebbins described polyploids as 'general purpose genotypes', which can tolerate a wide range of environmental conditions. However, little is known about its molecular basis because of the complexity of polyploid genomes. We hypothesized that allopolyploid species might(More)
One of the major issues in genome-wide association studies is to solve the missing heritability problem. While considering epistatic interactions among multiple SNPs may contribute to solving this problem, existing software cannot detect statistically significant high-order interactions. We propose software named LAMPLINK, which employs a cutting-edge(More)
Genome-wide association studies (GWASs) are widely used to investigate statistically significant associations between diseases and single nucleotide polymorphisms (SNPs) to identify causal factors of diseases. In GWAS, statistical significance of more than one million SNPs have been recently assessed, but in many case, no associations are found because of(More)