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

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
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updated by igor igor • written by biopat • biopat

1 answer

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?

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written by igor igor

Is that list applicable for mouse as well?

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written by GenoMax GenoMax

Good to know. Thanks!

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written by GenoMax GenoMax

What do I use as input file for PAM50?

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written by biopat • biopat

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.

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written by GenoMax GenoMax

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