Question

How to determine the breast cancer subtype based on mRNA data?

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7.7 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 • 2.6k views

ADD COMMENT • link updated 7.7 years ago by igor 13k • written 7.7 years ago by biopat • 0

score 0 · Answer 1 · 2016-08-02

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7.7 years ago

igor 13k

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 • link 7.7 years ago by igor 13k

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Is that list applicable for mouse as well?

ADD REPLY • link 7.7 years ago by GenoMax 141k

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

ADD REPLY • link 7.7 years ago by igor 13k

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Good to know. Thanks!

ADD REPLY • link 7.7 years ago by GenoMax 141k

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What do I use as input file for PAM50?

ADD REPLY • link 7.7 years ago by biopat • 0

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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 • link 7.7 years ago by GenoMax 141k