Hi rainerpac,
You have selected an interesting and relevant project! Your question, "Is there a difference in gene expression of certain genes between cancer and normal tissue?" is exactly the type of question that can be answered with this project. So you are on the right track.
First, let's distinguish between an over-expressed gene and an under-expressed gene. Both of these terms refer to gene expression relative to normal cells. Thus, an
over-expressed gene will be expressed (transcribed and translated into the protein product)
more in the cancerous tissue than in the normal tissue. An
under-expressed gene will be expressed (transcribed and translated)
less in the cancerous tissue than in the normal tissue.
When you are following the protocol, keep in mind that
Pool A refers to the
normal tissue, and
Pool B is the
cancerous tissue. So, an over-expressed gene will have more "tags" in column B than column A, where as an under-expressed gene will have fewer "tags" in column B than column A. If a gene is normally "off" but gets turned "on" in cancer cells, there will be zero tags in column A and a number in column B. If a gene is normally expressed but gets turned off in cancer cells, there will be a number in column A and a zero in column B.
I hope that helps you get started. I recommend going into the program and trying to follow the steps so you can get familiar with the procedure. Please post again (in this same thread) if you have more questions!
Heather