Question: Allele Specific Events
1
gravatar for Honglang Wang
6.6 years ago by
U.S.A
Honglang Wang10 wrote:

I am struggling with what kind of analysis belongs to allele specific level. What is the exact meaning of allele specific gene expression? If we got bunch of SNPs in some gene, could we say there are bunch of alleles of this gene? If this is the case, are we always doing the analysis which is allele specific? I am really lost in the concepts. I really want to know what kind of events are called allele specific and if we want to do allele specific gene expression data analysis, what is the data set looks like? Thanks in advance for helping this out.

allele • 5.9k views
ADD COMMENTlink modified 2.8 years ago by H.Hasani680 • written 6.6 years ago by Honglang Wang10

It also gets a bit difficult (as a bioinformatician) with the confusing usage of the word "allele"

ADD REPLYlink written 6.6 years ago by Arun2.3k

I upvoted this, because I think that some questions regarding some biological fundamentals are rather important for bioinformatics too. Since many of us deal with tools/databases that handle SNPs, it seems rather important to know about alleles and the confusion surrounding them.

ADD REPLYlink written 6.6 years ago by Joachim2.8k
6
gravatar for Mikael Huss
6.6 years ago by
Mikael Huss4.6k
Stockholm
Mikael Huss4.6k wrote:

Let's say you have a heterozygous SNP, which means two different alleles in the same position in the DNA. However, it may happen that only one of these alleles is transcribed into mRNA. This is referred to as allele specific expression. For instance, in women, one of the copies of the X chromosome is typically inactivated, so one expects to see only the alleles from the active X chromosome in the mRNA.

ADD COMMENTlink written 6.6 years ago by Mikael Huss4.6k
1

The terminology is also often used when it comes to things like variants within transcription factor binding sites, promoters, etc so you get differential expression levels between alleles in the genome. Also, be wary because often we use allele a bit incorrectly in that a person always has two alleles of a given gene. However, if they have two identical copies, that is really just two copies of the same allele (homozygosity). Allele is supposed to refer to a specific variant of a gene, but is often used to refer to a gene on one of the two parental chromosomes.

ADD REPLYlink written 6.6 years ago by Dan Gaston7.1k
2
gravatar for H.Hasani
2.8 years ago by
H.Hasani680
Freiburg, Germany
H.Hasani680 wrote:

I found this great talk from John Marioni, Research Group Leader in Computational Biology at EMBL-EBI

Very well explained.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by H.Hasani680

Thanks for sharing this nice talk!

ADD REPLYlink written 2.7 years ago by Dtriumph30
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