Gene Expression Signatures For Basal Vs Mesenchymal Breast Tumors?

Question

[user]

is there a canonical gene expression signature for a 'mesenchymal' breast tumor type versus a 'basal' breast tumor type? unsupervised gene expression clustering in primary breast tumors using PAM50 gene set often reveals five tumor subtypes (basal, her2, luminal a, luminal b and normal-like) but it's not clear how similar or dissimilar basal tumors would be to mesenchymal tumors (i.e. tumors with high vimentin/fibronectin1/snail/twist and low epithelial markers like ecadherin). Is there a canonical gene list for both types and perhaps associated paper that tries to use gene expression to answer what the differences between the two types are?

I could only find (http://www.ncbi.nlm.nih.gov/pubmed/20021961) which does not use genome wide expression analysis and is not conclusive

Answer 1

[David Westergaard]

I honestly don't think you will find a canonical gene expression signature for anything (do correct me if I'm wrong.) See e.g. this comment from 2003, and that's in controlled cell cultures. Outside the in vitro environment, there are a lot more factors which can influence the gene expression, just to mention a few:

• Diet
• Smoking
• Age
• Nationality/ethnicity
• Individual mutations

And the list goes on. That being said, if you have the gene expression data for your tumor lines of interest, you can just go ahead an analyse it yourself. If it's all from Affymetrix chips, you can probably use the frozen RMA approach, otherwise maybe virtualArray is useful.