ArticleBMC genomics2006
Cis-regulatory variations: a study of SNPs around genes showing cis-linkage in segregating mouse populations.
Article in BMC genomics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 44 citations in OpenAlex.
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- Gene expression in large pedigrees: analytic approaches.BMC genetics · 2016Article
- Candidate gene association studies: a comprehensive guide to useful in silico tools.BMC genetics · 2013Review
- Insights into the regulation of human CNV-miRNAs from the view of their target genes.BMC genomics · 2012Article
- Effect of normalization on statistical and biological interpretation of gene expression profiles.Frontiers in genetics · 2012Article
- Genetics and regulatory impact of alternative polyadenylation in human B-lymphoblastoid cells.PLoS genetics · 2012Article
- Divergent and nonuniform gene expression patterns in mouse brain.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
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- Using transcriptome profiling to characterize QTL regions on chicken chromosome 5.BMC genomics · 2009Article
- Analytical methods for inferring functional effects of single base pair substitutions in human cancers.Human genetics · 2009Review
- Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP.Nucleic acids research · 2009Article
- High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues.Genome research · 2009Article
- Susceptibility loci for murine HIV-associated nephropathy encode trans-regulators of podocyte gene expression.The Journal of clinical investigation · 2009Article
- Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast.PLoS computational biology · 2009Article
- Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance.Molecular systems biology · 2009Article
- Extent of differential allelic expression of candidate breast cancer genes is similar in blood and breast.Breast cancer research : BCR · 2009Article
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Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundChanges in gene expression are known to be responsible for phenotypic variation and susceptibility to diseases. Identification and annotation of the genomic sequence variants that cause gene expression changes is therefore likely to lead to a better understanding of the cause of disease at the molecular level. In this study we investigate the pattern of single nucleotide polymorphisms (SNPs) in genes for which the mRNA levels show cis-genetic linkage (gene expression quantitative trait loci mapping in cis, or cis-eQTLs) in segregating mouse populations. Such genes are expected to have polymorphisms near their physical location (cis-variations) that affect their mRNA levels by altering one or more of the cis-regulatory elements. This led us to characterize the SNPs in promoter (5 Kb upstream) and non-coding gene regions (introns and 5 Kb downstream) (cis-SNPs) and the effects they may have on putative transcription factor binding sites.
resultsWe demonstrate that the cis-eQTL genes (CEGs) have a significantly higher frequency of cis-SNPs compared to non-CEGs (when both sets are taken from the non-IBD regions, i.e. regions not identical by descent). Most CEGs having cis-SNPs do not contain these SNPs in the phylogenetically conserved regions. In those CEGs that contain cis-SNPs in the phylogenetically conserved regions, enrichment of cis-SNPs occurs both within and outside of the conserved sequences. A higher fraction of CEGs are also seen to harbor cis-SNP that affect predicted transcription factor binding sites, a likely consequence of the higher cis-SNPs density in these genes.
conclusionThis present study provides the first genome-wide investigation of the putative cis-regulatory variations in a large set of genes whose levels of expression give rise to cis-linkage in segregating mammalian populations. Our results provide insights into the challenges that exist in identifying polymorphisms regulating gene expression using bioinformatic sequence analysis approaches. The data provided herein should benefit future investigations in this area.
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