Forum:Confusion Related To A Term Probe-By-Background Interaction

Question

[mtyler.jason]

I was reading a paper related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, using the gene expression of the cells a predictor of the drug response is created.

They have stated that just using the correlation between the gene expression and the drug response might not be a good predictor. But the genes interact through signaling pathways to drive a particular drug response.

What these guys have done is like used PCA on the gene expressions of the cancer cells to use the components which preserve the greatest variance.

Actually, I didn't get what they mean by probe-by-background interaction and how it is calculated. I am attaching the screenshots of the paper.

Can anyone please explain. I googled for a while but didn't get it.

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[Michael Kuhn]

cross-posted with Bio.SE: http://biology.stackexchange.com/questions/7800/confusion-related-to-a-term-probe-by-background-interaction

[VS]

The paper is behind a paywall and I cannot find the attached screenshots you mention. Can you check?

[mtyler.jason]

ok I have added the screenshots of the paper

Answer 1

[VS]

Ok, I have seen the screenshots. Googling for the term 'probe-by-background' is not going to help you because it is a name given by them to their method for predicting patient responses to drug based on gene expression profiles. It is explained in the very paper that you are reading. To explain the term, we might have to read the full paper for you!