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| Yupeng Wang; Sandeep J. Joseph; Xinyu Liu; Michael Kelly; Romdhane Rekaya. |
| Recently, gene co-expression relationships have been found to be often conditional and dynamic. Besides, many studies have suggested that single nucleotide polymorphisms (SNPs) have impacts on gene expression variations in human populations. The SNPxGE2 database contains the computationally predicted human 3-way SNP-expression associations, that is, the differential co-expression between 2 genes is associated with a genotype/SNP. This data was generated from a large scale association study that was based on the HapMap data, which covered 269 individuals from 4 human populations, 701,202 SNPs and 15,000 gene expression profiles. Two models of 3-way SNP-expression associations were considered: gap/substitution and on/off. The implementation was carried out... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5704/version/1 |
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| Yupeng Wang; Xinyu Liu; Romdhane Rekaya. |
| Genome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO pheromones. By looking... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6994/version/1 |
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