Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test
dc.contributor.author | Peralta, J. | |
dc.contributor.author | Almeida, M. | |
dc.contributor.author | Abraham, L. | |
dc.contributor.author | Moses, Eric | |
dc.contributor.author | Blangero, J. | |
dc.date.accessioned | 2017-04-28T13:59:28Z | |
dc.date.available | 2017-04-28T13:59:28Z | |
dc.date.created | 2017-04-28T09:06:09Z | |
dc.date.issued | 2016 | |
dc.identifier.citation | Peralta, J. and Almeida, M. and Abraham, L. and Moses, E. and Blangero, J. 2016. Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test. | |
dc.identifier.uri | http://hdl.handle.net/20.500.11937/52638 | |
dc.identifier.doi | 10.1186/s12919-016-0013-1 | |
dc.description.abstract |
© 2016 The Author(s).We present a novel approach to detect potential cis-acting regulatory loci that combines the functional potential, an empirical DNase-seq based estimate of the allele-specificity of DNase-I hypersensitivity sites, with kernel-based variance component association analyses against expression phenotypes. To test our method we used public ENCODE whole genome DNase-I sequencing data, from a single sample, to estimate the functional potentials of the subset of 10,552 noncoding heterozygous single-nucleotide polymorphisms (SNPs) that were also present in the Genetic Analysis Workshop 19 (GAW19) family-based data set. We then built two covariance kernels, one nonweighted and one weighted by the functional potentials, and conducted kernel-based variance component association analyses against the 20,527 transcript expression phenotypes in the GAW19 family-based data set. We found signals of potential cis-regulatory effects, that surpassed the Bonferroni significance threshold, for ten transcripts. Stepwise removal of the cis-located SNPs from the weighted kernel lead to the disappearance of the association signal from our top transcript hit. We found compelling evidence of allele-specific cis-regulation for four transcripts using both kernels, and our results agree with previous research that suggests the involvement of specific cis-located variants in the regulation of their neighboring gene. | |
dc.title | Finding potential cis-regulatory loci using allele-specific chromatin accessibility as weights in a kernel-based variance component test | |
dc.type | Conference Paper | |
dcterms.source.volume | 10 | |
dcterms.source.issn | 1753-6561 | |
dcterms.source.title | BMC Proceedings | |
dcterms.source.series | BMC Proceedings | |
curtin.department | School of Biomedical Sciences | |
curtin.accessStatus | Open access via publisher |
Files in this item
Files | Size | Format | View |
---|---|---|---|
There are no files associated with this item. |