ArticleBMC genomics2014
Allele-specific expression and eQTL analysis in mouse adipose tissue.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed.
- Statistical framework for calling allelic imbalance in high-throughput sequencing data.Nature communications · 2025Article
- Machine learning on alignment features for parent-of-origin classification of simulated hybrid RNA-seq.BMC bioinformatics · 2024Article
- Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs.BMC genomics · 2024Article
- Fat-tail allele-specific expression genes may affect fat deposition in tail of sheep.PloS one · 2024Article
- SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.Genome biology · 2023Article
- Genetic variation in histone modifications and gene expression identifies regulatory variants in the mammary gland of cattle.BMC genomics · 2022Article
- DeCAF: a novel method to identify cell-type specific regulatory variants and their role in cancer risk.Genome biology · 2022Article
- BrewerIX enables allelic expression analysis of imprinted and X-linked genes from bulk and single-cell transcriptomes.Communications biology · 2022Article
- Uncovering Divergence in Gene Expression Regulation in the Adaptation of Yeast to Nitrogen Scarcity.mSystems · 2021Article
- Increased hypospadias risk byAging · 2021Article
- Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT.Scientific reports · 2021Article
- Article
- Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits.Genetics, selection, evolution : GSE · 2020Article
- Sex differences in human adipose tissue gene expression and genetic regulation involve adipogenesis.Genome research · 2020Article
- Strategies for eQTL mapping in allopolyploid organisms.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- Tumor suppressor genes and allele-specific expression: mechanisms and significance.Oncotarget · 2020Article
- cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel.Genome biology · 2020Article
- ISoLDE: a data-driven statistical method for the inference of allelic imbalance in datasets with reciprocal crosses.Bioinformatics (Oxford, England) · 2020Article
- Leveraging allelic imbalance to refine fine-mapping for eQTL studies.PLoS genetics · 2019Article
- Allele-Specific Expression of CD4Genes · 2019Article
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7 authors.
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Abstract
backgroundThe simplest definition of cis-eQTLs versus trans, refers to genetic variants that affect expression in an allele specific manner, with implications on underlying mechanism. Yet, due to technical limitations of expression microarrays, the vast majority of eQTL studies performed in the last decade used a genomic distance based definition as a surrogate for cis, therefore exploring local rather than cis-eQTLs.
resultsIn this study we use RNAseq to explore allele specific expression (ASE) in adipose tissue of male and female F1 mice, produced from reciprocal crosses of C57BL/6J and DBA/2J strains. Comparison of the identified cis-eQTLs, to local-eQTLs, that were obtained from adipose tissue expression in two previous population based studies in our laboratory, yields poor overlap between the two mapping approaches, while both local-eQTL studies show highly concordant results. Specifically, local-eQTL studies show ~60% overlap between themselves, while only 15-20% of local-eQTLs are identified as cis by ASE, and less than 50% of ASE genes are recovered in local-eQTL studies. Utilizing recently published ENCODE data, we also find that ASE genes show significant bias for SNPs prevalence in DNase I hypersensitive sites that is ASE direction specific.
conclusionsWe suggest a new approach to analysis of allele specific expression that is more sensitive and accurate than the commonly used fisher or chi-square statistics. Our analysis indicates that technical differences between the cis and local-eQTL approaches, such as differences in genomic background or sex specificity, account for relatively small fraction of the discrepancy. Therefore, we suggest that the differences between two eQTL mapping approaches may facilitate sorting of SNP-eQTL interactions into true cis and trans, and that a considerable portion of local-eQTL may actually represent trans interactions.
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