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Of the 192 target genes, 79 map to a significant eQTL or pQTL in at least one dietary condition.

is the line for a paper "Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population"

As far as I know an eQTL is a SNP (particular genotype) affects gene expression. How can I map then a gene to an eQTL? A gene is a sequence on a reference genome. Genotypes of one specific gene are just variations of the sequence of this specific gene. So, a gene itself cannot be an eQTL, a specific genotype (with a variation) can be, right?

So, how can it be possible that one gene (let say GENE22, location: 10-100) is mapped to eQTL(SNP within GENE22, location: 12) in one dietary condition but is not mapped to eQTL in another dietary condition if we are still speaking about the same gene and the same location of an eQTL? So, I am not quite sure what they mean or what they mapped there.

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  • $\begingroup$ The QTL is a locus in which the genes/markers have been correlated with some phenotype. It may include markers such as SNPs but they are not SNPs in themselves. A gene can be part of a QTL, but the QTL itself is made up of a number of markers! $\endgroup$ – CKM Aug 27 '15 at 22:40
  • $\begingroup$ "but they are not SNPs in themselves." There are studies that have lists of eQTLs as SNPs. "A gene can be part of a QTL but the QTL itself is made up of a number of makers". So, you want to say, that they had a list of eQTLs and pQTLs and they just looked in which genes they are located, right? It does not make sense for me because they are referring to dietary conditions and if the looked only at the location then there should not be differences in the conditions because location is always the same. $\endgroup$ – Alina Aug 27 '15 at 23:06
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You take a list of SNPs and a list of gene expression values and you plug it into something like this: http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/

So, how can it be possible that one gene (let say GENE22, location: 10-100) is mapped to eQTL(SNP within GENE22, location: 12) in one dietary condition but is not mapped to eQTL in another dietary condition if we are still speaking about the same gene and the same location of an eQTL? So, I am not quite sure what they mean or what they mapped there.

The SNP is associated with expression level changes in that gene for one dietary condition but that same SNP is not associated with expression level changes in another dietary condition. Its possible that the SNP never appears in samples from the other dietary condition.

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  • $\begingroup$ I edited my question. $\endgroup$ – Alina Aug 27 '15 at 23:18
  • $\begingroup$ so, the right way would be to say: "markers within 79 genes map to a significant ...." , right? $\endgroup$ – Alina Aug 27 '15 at 23:48
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    $\begingroup$ I'm not sure the phrasing for which is significant, my guess would be something like: "we find X significant eQTLs when testing Y genes and Z snps" $\endgroup$ – yingw Aug 28 '15 at 18:43

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