I conducted a differential gene expression analysis on a RNA-seq dataset to evaluate the alterations coming from the knockout of only one protein coding gene (comparison = knockout versus wildtype). Of a total of 88 upregulated genes, 73 are located on the same chromosome. I have already looked at the positions of the upregulated genes inside the chromosome and they are spread through all the chromosome. Besides, I checked for their functions and they don't seem to be functionally related. One possible explanation could be an extra copy of the chromosome (as the organism presents aneuploidy), but this is not an usual chromosome known to deviate from the diploid pattern. I'm waiting for a wet lab experiment to check ploidy anyway.
But, I would like to know if it could it be an artifact? If so, how can I check it?