[BioC] 217216_x_at is NOT dihydrolipoamide S-succinytransferase
kdawson at ucdavis.edu
Wed Mar 30 01:58:25 CEST 2005
Apparently my previous message did not appear on the Bioconductor list serve
due to its attachment. I think, Robert should have received it though.
The annotation error was caused by the fact that DLAT and MLH3 are close
neighbors on chromosome 14 and at one point, somebody used the same locus
info for both. I cannot attach an image that appears on the list serve;
therefore, probably, the easiest way to be demonstrate what I am talking
about is if you do the followings:
(1) Go to affymetrix.com and go to NetAffy
(2) Look up 217216_x_at. It will tell you, it refers to MLH3.
(3) Click on <details>
(4) At the alignments, click on the chr14 entry: This will take you to the
UCSC genome browser with the Affymetrix probe set information aligned with
the gene information
(5) Extend the chromosomal location to chr14:74,422,000-74,600,000 to see
both genes at a time.
On the left side of the map, you'll see DLST, and on the right side you'll
see MLH3. The 217216_x_at probeset matches MLH3 and NOT DLST.
A second problem caused by the misannotation is that in the annotation
packages, the 215210_s_at is annotating the DLST pseudogene. It is true that
the probeset also matches the pseudogene on chromosome 1; however it
primarily matches DLST itself on chromosome 14. That is why I am suggesting
to clarify the issues and change the annotation of 215210_s_at to DLST and
the annotation of 217216_x_at to MLH3 as described in my previous post
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