Question: Use cmap with rna-seq results
0
gravatar for bioinformatics
2.7 years ago by
bioinformatics0 wrote:

Hello World,

I would like to find links between drugs and the differentially expressed genes we found.

I want to use cmap (https://portals.broadinstitute.org/cmap/index.jsp) with genes that are up and down regulated. These genes were calculated using RNA-seq.

Does someone know if it is possible to use RNA-seq with the cmap tool ?

I need to use grp files, which on their site it says (http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#GRP):

That it is a set of gene names, which will not work when loaded into their cmap. In their example file it looks like :

213507_s_at
208975_s_at
201305_x_at
217027_x_at
217684_at
202613_at
213803_at
208974_x_at
201306_s_at
213573_at
202589_at

How can i convert gene names into this ?

I am very great full for any help with this problem !

Regards,

Tim

rna-seq • 1.1k views
ADD COMMENTlink written 2.7 years ago by bioinformatics0

Those look like Agilent ID's?

These are affynetrix ID's so a query here: https://www.affymetrix.com/analysis/index.affx

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by genomax72k

A: How to upload my own database on CMAP

ADD REPLYlink written 2.7 years ago by Zhilong Jia1.5k

I found that the probe set: The collection of match and mismatch oligonucleotides on an Affymetrix GeneChip microarray. So i think i have to convert the genes to Affymetrix , does anyone know how ?

ADD REPLYlink written 2.7 years ago by bioinformatics0
1

A batch query here: https://www.affymetrix.com/analysis/index.affx You will need to create an account if you don't have one.

ADD REPLYlink written 2.7 years ago by genomax72k

Hey thanks man ! I think i got it working now.

ADD REPLYlink written 2.7 years ago by bioinformatics0
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