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.
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.