Question: How to determine the breast cancer subtype based on mRNA data?
0
gravatar for pat.longjump
3.1 years ago by
pat.longjump0 wrote:

Hi,

I recently got RNAseq data back of mouse mammary tumors. Now I would like to classify what kind of breast cancer subtype it is (Luminal A, Luminal B, basal, etc.) based on the RNA expression. How would I approach this? Will I need a WT mammary gland to compare it to? If anyone could point me in the right direction that would be awesome!

Thank you!

Pat

cancer rna-seq breast subtype mrna • 1.4k views
ADD COMMENTlink modified 3.1 years ago by igor8.3k • written 3.1 years ago by pat.longjump0
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gravatar for igor
3.1 years ago by
igor8.3k
United States
igor8.3k wrote:

You don't need the WT. There is a PAM50 gene signature that is commonly used. See this previous discussion: Where To Download Pam50 Gene Set?

ADD COMMENTlink written 3.1 years ago by igor8.3k

Is that list applicable for mouse as well?

ADD REPLYlink written 3.1 years ago by genomax71k

At least according to this paper: http://dx.doi.org/10.1371/journal.pone.0072287

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by igor8.3k

Good to know. Thanks!

ADD REPLYlink written 3.1 years ago by genomax71k

What do I use as input file for PAM50?

ADD REPLYlink written 3.1 years ago by pat.longjump0
1

PAM50 is a list of diagnostic genes. See @Joelsparker1's (author of PAM50 paper) answer (and the papers he refers to) in the thread @igor linked above. You may have to translate human gene names to mouse for your use.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by genomax71k
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