Question: Unknown gene names in pd.clariom.d.human annotation package
gravatar for Antonio Ahn
17 months ago by
Antonio Ahn10
University of Otago
Antonio Ahn10 wrote:

I have performed a differential gene expression (DEG) analysis using the Clariom D human microrray and pd.clariomd.human (affymetrix-provided) annotation package. In the top 100 DEG list, there are many gene names in lower-case letters that I am unable to identify. This includes names such as "shasmar", "tusweyb", "flybler.1" and "nugo". Would anyone tell me what these are? 

Thank you! 

ADD COMMENTlink modified 17 months ago by James W. MacDonald50k • written 17 months ago by Antonio Ahn10
Answer: Unknown gene names in pd.clariom.d.human annotation package
gravatar for James W. MacDonald
17 months ago by
United States
James W. MacDonald50k wrote:

The annotation packages for Affymetrix arrays are provided by us as a convenience (they are simply a reformatted version of the data that Affy supplies to the wider community) without any checking or vetting on our part. So any answer you get here is likely to be due to somebody going to and looking it up for you, which you can do yourself just as easily and without having to wait.

I actually did look up shasmar, and it is apparently something that AceView says is a thing. And the FAQ for AceView starts with the question 'Are AceView transcripts reliable?' and they then spend like 5 paragraphs explaining that they in fact are. Which paradoxically makes me think the opposite?

Anyway, it seems that AceView likes to use these cute all lower case names for whatever thing they come up with that NCBI and Ensembl seem not to believe in, so dollars to donuts those are all AceView-only transcripts of some sort.

ADD COMMENTlink written 17 months ago by James W. MacDonald50k
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