Question

Info Needed Regarding Gene Id Conversion From Agilent To Others

1

Entering edit mode

14.7 years ago

Mehraj ▴ 30

I am using Agilent-014850 4x44k and I am analysing the data on genespring. I am also doing manual search of some specific genes to determine their expression levels. I am facing lots of problems with gene IDs.

I tried using DAVID (April 09, 2010) also, but there are hundreds of agilent ids not recognized by DAVID.

Also can any one find me agilent id for MRC1 (mannose receptor, C type 1) gene (human), please. I could find only MRC1L1, MRC3 and MRC2.

identifiers conversion • 5.5k views

ADD COMMENT • link updated 12 months ago by Ram 44k • written 14.7 years ago by Mehraj ▴ 30

0

Entering edit mode

@Mehraj Please consider rephrasing as a question and being specific about what you want help with in order to get meaningful replies. Cheers.

ADD REPLY • link 14.7 years ago by Eric Normandeau 11k

Ram · Answer 1 · 2010-04-12

3

Entering edit mode

14.7 years ago

Yuri ★ 1.7k

Related question: Gene Id Conversion Tool

ADD COMMENT • link updated 5.3 years ago by Ram 44k • written 14.7 years ago by Yuri ★ 1.7k

score 3 · Answer 2 · 2010-08-31

3

Entering edit mode

14.3 years ago

Nina ▴ 30

Hi,

I have the same problem with MRC1. A_23_P12746 is the Agilent ID for MRC1L1. Did you find the ID? Or does it not exsist (which would be strange)? Thanks

ADD COMMENT • link 14.3 years ago by Nina ▴ 30

0

Entering edit mode

Hi Nina. Given that the question was asked in april and that it was Mehraj's only contribution to the forum, I do not believe that you will receive an answer from him. However, please feel free to post a clear question to the forum yourself. Be sure to give more than enough details about what you are trying to do in order to receive good answers. Cheers

ADD REPLY • link 14.3 years ago by Eric Normandeau 11k

score 2 · Answer 3 · 2010-04-12

Can't you summarize your results in terms of gene symbols or other gene ids and then use those with other tools like DAVID? You should have agilent annotation files that allow you to translate probe ids into genes.

In terms of a gene not being represented on the array, that is best solved by looking at the annotation files provided by Agilent and contacting them if you have a question.

score 1 · Answer 4 · 2010-04-12

1

Entering edit mode

14.7 years ago

Paulo Nuin ★ 3.7k

One easy way to convert different ids from different sources is to use Martview in Biomart's website. Just upload a file with your IDs as a filter set and get some other ID as a result in the features set. But without more information is difficult to give you a correct answer.

ADD COMMENT • link 14.7 years ago by Paulo Nuin ★ 3.7k

Ram · Answer 5 · 2010-04-13

I had similar issues with Affy array, as suggested mmarchin and nuin, you may start with the conversion using DAVID or BioMart. I would also recommend you to check the latest annotation file from Agilent as well.

I have tried for the MRC-1 in BioMart using HGNC ID. Agilent wholegenome ID is A_23_P12746: http://www.biomart.org/biomart/martview/7312850d734d8b6436f1a79969cf1ab2.