Abstract
Knowledge about how changes in gene expression are encoded by expression quantitative trait loci (eQTLs) is a key to construct the genotype-phenotype map for complex traits or diseases. Traditional eQTL mapping is to associate one transcript with a single marker at a time, thereby limiting our inference about a complete picture of the genetic architecture of gene expression. Here, we implemented an ultrahigh-dimensional variable selection model to build a computing platform that can systematically scan main effects and interaction effects among all possible loci and identify a set of significant eQTLs modulating differentiation and function of gene expression. This platform, named iFORM/eQTL, was assembled by forward-selection-based procedures to tackle complex covariance structures of gene-gene interactions. iFORM/eQTL can particularly discern the role of cis-QTLs, trans-QTLs and their epistatic interactions in gene expression. Results from the reanalysis of a published genetic and genomic data set through iFORM/eQTL gain new discoveries on the genetic origin of gene expression differentiation in Caenorhabditis elegans, which could not be detected by a traditional one-locus/one-transcript analysis approach.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 250-259 |
| Number of pages | 10 |
| Journal | Briefings in Bioinformatics |
| Volume | 18 |
| Issue number | 2 |
| DOIs | |
| State | Published - Jan 1 2017 |
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All Science Journal Classification (ASJC) codes
- Information Systems
- Molecular Biology
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iFORM/eQTL : An ultrahigh-dimensional platform for inferring the global genetic architecture of gene transcripts. / Gosik, Kirk; Kong, Lan; Chinchilli, Vernon; Wu, Rongling.
In: Briefings in Bioinformatics, Vol. 18, No. 2, 01.01.2017, p. 250-259.Research output: Contribution to journal › Article
TY - JOUR
T1 - iFORM/eQTL
T2 - An ultrahigh-dimensional platform for inferring the global genetic architecture of gene transcripts
AU - Gosik, Kirk
AU - Kong, Lan
AU - Chinchilli, Vernon
AU - Wu, Rongling
PY - 2017/1/1
Y1 - 2017/1/1
N2 - Knowledge about how changes in gene expression are encoded by expression quantitative trait loci (eQTLs) is a key to construct the genotype-phenotype map for complex traits or diseases. Traditional eQTL mapping is to associate one transcript with a single marker at a time, thereby limiting our inference about a complete picture of the genetic architecture of gene expression. Here, we implemented an ultrahigh-dimensional variable selection model to build a computing platform that can systematically scan main effects and interaction effects among all possible loci and identify a set of significant eQTLs modulating differentiation and function of gene expression. This platform, named iFORM/eQTL, was assembled by forward-selection-based procedures to tackle complex covariance structures of gene-gene interactions. iFORM/eQTL can particularly discern the role of cis-QTLs, trans-QTLs and their epistatic interactions in gene expression. Results from the reanalysis of a published genetic and genomic data set through iFORM/eQTL gain new discoveries on the genetic origin of gene expression differentiation in Caenorhabditis elegans, which could not be detected by a traditional one-locus/one-transcript analysis approach.
AB - Knowledge about how changes in gene expression are encoded by expression quantitative trait loci (eQTLs) is a key to construct the genotype-phenotype map for complex traits or diseases. Traditional eQTL mapping is to associate one transcript with a single marker at a time, thereby limiting our inference about a complete picture of the genetic architecture of gene expression. Here, we implemented an ultrahigh-dimensional variable selection model to build a computing platform that can systematically scan main effects and interaction effects among all possible loci and identify a set of significant eQTLs modulating differentiation and function of gene expression. This platform, named iFORM/eQTL, was assembled by forward-selection-based procedures to tackle complex covariance structures of gene-gene interactions. iFORM/eQTL can particularly discern the role of cis-QTLs, trans-QTLs and their epistatic interactions in gene expression. Results from the reanalysis of a published genetic and genomic data set through iFORM/eQTL gain new discoveries on the genetic origin of gene expression differentiation in Caenorhabditis elegans, which could not be detected by a traditional one-locus/one-transcript analysis approach.
UR - http://www.scopus.com/inward/record.url?scp=85018762565&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85018762565&partnerID=8YFLogxK
U2 - 10.1093/bib/bbw014
DO - 10.1093/bib/bbw014
M3 - Article
C2 - 26944084
AN - SCOPUS:85018762565
VL - 18
SP - 250
EP - 259
JO - Briefings in Bioinformatics
JF - Briefings in Bioinformatics
SN - 1467-5463
IS - 2
ER -