How to determine the breast cancer subtype based on mRNA data?
1
0
Entering edit mode
5.3 years ago
biopat • 0

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

RNA-Seq Cancer Breast mRNA subtype • 2.1k views
ADD COMMENT
0
Entering edit mode
5.3 years ago
igor 12k

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 COMMENT
0
Entering edit mode

Is that list applicable for mouse as well?

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Good to know. Thanks!

ADD REPLY
0
Entering edit mode

What do I use as input file for PAM50?

ADD REPLY
1
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 1800 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6