Question: gene expression in disease and normal
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gravatar for rob.costa1234
2.8 years ago by
rob.costa1234170
United States
rob.costa1234170 wrote:

I am stuck with a problem that is more of a trouble shooting with basic understanding rather than using any software/ statistical package. I want to show that a signature of 10 genes can be differentially expressed in disease patients tissue samples while such genes are not affected in healthy individuals. This is a simple gene expression affymatrix data and I have 20 replicates (patients with disease) ad 10 healthy individuals.

ADD COMMENTlink modified 2.8 years ago by Devon Ryan91k • written 2.8 years ago by rob.costa1234170

Where did you come up with the number 10 (for genes of interest)?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax69k

these 10 genes are known biomarker genes which have been identified in various previous publications. so now what I would like to show that these gene show expression pattern in disease state but remain unaffected in non-disease state.

ADD REPLYlink written 2.8 years ago by rob.costa1234170
1

And you are not able to show them as DE in your dataset? Is there at least a subset of them that are showing up or none do?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax69k
0
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

The simplest method would be gene set enrichment with something like GSEA. If these are really biomarkers then you'd presumably like them to be individually differentially expressed as well, but if the heterogeneity is high enough or the controls aren't matched well enough then this could be problematic (of course, they shouldn't be considered biomarkers then...or the array just sucks at measuring them).

ADD COMMENTlink written 2.8 years ago by Devon Ryan91k
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