Just need a answer, no need for explannation. You observe differential expressio
ID: 78468 • Letter: J
Question
Just need a answer, no need for explannation.
You observe differential expression of a gene between two individuals. A close look at their genomes indicates there is a single nucleotide polymorphism (SNP) close to the 5' end of the gene and a second SNP approximately 15 kb away. Which SNP caused the differential expression? The promoter proximal SNP (the one close to the 5' end of the gene). It is impossible to know from this information. The distal (15kb away) SNP, as it is an enhancer. Neither, the differential expression HAD to be caused by something else. You are comparing the expression from a benign tumor to the normal adjacent cells. You have run RNA-seq in duplicate and determined that the oncogene ohNo1 is dramatically overexpressed in the tumor. However, upon closer examination, the two replicates give very different estimates for OhNo1, so you decide to do more replicates. Across many replicates it is clear that OhNo1 expression levels are highly variable. How does this knowledge influence your original conclusion that OhNo1 is overexpressed? As long as the max value in the normal tissue is smaller than the min value in the tumor, you can be confident that OhNo1 is overexpressed. You can never call a gene with high variance as confidently differentially expressed. With high variance, your confidence in OhNo1 being different is less secure. As long as the average of the tumor samples is higher than the average of the normal cells, you can be confident that OhNo1 is overexpressed.Explanation / Answer
Q1. Which SNP caused the differential expression cannot be found with this information alone as there are some SNP that are cis-acting so the correct option is:
It is impossible to know from this information.
Q2: With high variance, our confidence in OhNo1 being different is less secure. This is the correct option as we cannot have confidence in something that varies.
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