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
0 answers
No answers yet.
Log in to answer this question.
Those look like
AgilentID's?These are affynetrix ID's so a query here: https://www.affymetrix.com/analysis/index.affx
A: How to upload my own database on CMAP
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 ?
A batch query here: https://www.affymetrix.com/analysis/index.affx You will need to create an account if you don't have one.
Hey thanks man ! I think i got it working now.