Unknown

Dataset Information

0

Mapping transcription mechanisms from multimodal genomic data.


ABSTRACT: Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data.We develop a method to identify eQTLs. The method represents eQTLs as information flux between genetic variants and transcripts. We use information theory to simultaneously interrogate SNP and gene expression data, resulting in a Transcriptional Information Map (TIM) which captures the network of transcriptional information that links genetic variations, gene expression and regulatory mechanisms. These maps are able to identify both cis- and trans- regulating eQTLs. The application on a dataset of leukemia patients identifies eQTLs in the regions of the GART, PCP4, DSCAM, and RIPK4 genes that regulate ADAMTS1, a known leukemia correlate.The information theory approach presented in this paper is able to infer the dependence networks between SNPs and transcripts, which in turn can identify cis- and trans-eQTLs. The application of our method to the leukemia study explains how genetic variants and gene expression are linked to leukemia.

SUBMITTER: Chang HH 

PROVIDER: S-EPMC2967743 | biostudies-literature | 2010 Oct

REPOSITORIES: biostudies-literature

altmetric image

Publications

Mapping transcription mechanisms from multimodal genomic data.

Chang Hsun-Hsien HH   McGeachie Michael M   Alterovitz Gil G   Ramoni Marco F MF  

BMC bioinformatics 20101028


<h4>Background</h4>Identification of expression quantitative trait loci (eQTLs) is an emerging area in genomic study. The task requires an integrated analysis of genome-wide single nucleotide polymorphism (SNP) data and gene expression data, raising a new computational challenge due to the tremendous size of data.<h4>Results</h4>We develop a method to identify eQTLs. The method represents eQTLs as information flux between genetic variants and transcripts. We use information theory to simultaneou  ...[more]

Similar Datasets

| S-EPMC6192561 | biostudies-literature
| S-EPMC3813840 | biostudies-other
| S-EPMC7728399 | biostudies-literature
| S-EPMC7167350 | biostudies-literature
| S-EPMC5860202 | biostudies-literature
| S-EPMC6120357 | biostudies-literature
| S-EPMC4666734 | biostudies-literature
| S-EPMC8081343 | biostudies-literature
| S-EPMC1804257 | biostudies-literature
| S-EPMC4189582 | biostudies-literature