This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Converted Agilent Probe IDs to NCBI IDs in sheep (ovis aries)

Hello,

I've done some work on sheep using an Agilent 8x15k array but am having difficulty converting the Agilent probe IDs into a useable NCBI ID for functional annotation and clustering.

It seems someone else had this issue awhile ago and you can see the post here: How To Convert Gene Names From Agilent Id To Ncbi Ids?

I've tried to follow the advice that user Neilfws wrote but I'm not sure how to use the GPL14112 data table in David to convert my IDs. If someone has done this before or knows of a good guide that I could follow that would be great.

conversion genespring agilent microarray
• 2,477 views • link
written by jibriil.ibrahim • jibriil.ibrahim

You should be able to find annotation for this array at Agilent's eArray site (free account needed).

• 0 views • link
written by GenoMax GenoMax

Great, I'll look now. Thanks very much.

Edit: Unfortunately it looks like they don't offer sheep.

• 0 views • link
written by jibriil.ibrahim • jibriil.ibrahim

From the page linked above click on the "Catalog gene lists" link in top right quadrant (under "Important links"). Once you get the next page click on page 2. Sheep array is listed under design (# 019921). Click on the "gene lists" link on the right to get the gene list annotations.

A small sample of what you will get:

ProbeID TargetID    GeneSymbol  GeneName    Accessions  Description
A_70_P041221    AB005283    SLC2A4  solute carrier family 2 member 4    gb|AB005283|ref|XM_012185632|tc|TC54459 PREDICTED: Ovis aries solute carrier family 2 (facilitated glucose transporter), member 4 (SLC2A4), transcript variant X1, mRNA [XM_012185632]
A_70_P041222    AB005283    SLC2A4  solute carrier family 2 member 4    gb|AB005283|ref|XM_012185632|tc|TC54459 PREDICTED: Ovis aries solute carrier family 2 (facilitated glucose transporter), member 4 (SLC2A4), transcript variant X1, mRNA [XM_012185632]
• 0 views • link
written by GenoMax GenoMax

You're right, I can see it now and have the file, how do I use this though to convert my list which only has probe IDs to one that is more comprehensive and includes other IDs though?

• 0 views • link
written by jibriil.ibrahim • jibriil.ibrahim

0 answers

No answers yet.

Log in to answer this question.

More posts like this