Please understand that the experts on this forum do not necessarily check the forum every day, so sometimes it takes awhile to get a response.
I also want to point out that this project is rated at a difficulty of 9, which means that it is quite difficult and usually meant for a high-school level project. That doesn't mean that you should not move forward with it; but it may explain some of your frustration.
Your hypothesis is going to be a prediction of what you think you might find. Donna already gave you the link to ScienceBuddies' excellent information about how to write a hypothesis. We cannot make one for you; it has to come from what you are interested in doing. One example would be for you to predict that two types of cancer would have similar genes that are overexpressed.
KATHY030 wrote:I also need help what does this mean [ A > B ] [ A < B ] ?
According to the instructions, B is the pool of genes from cancerous tissue and A is the pool of genes from normal tissue. [ A > B ] would mean that the normal tissue expresses that gene more than the cancerous tissue. [ A < B] would mean the normal tissue expresses that gene less than the cancerous tissue.
KATHY030 wrote:What is a tag I din't understand that?
A tag is a DNA sequence used to find the gene. It's basically a small part of the gene used to identify its expression. Here is how the project defines it:
Tag refers to the short nucleic acid sequence that identifies the gene. There is one tag for each copy of the gene. The more tags there are in a library, the more copies of that gene product (mRNA) there are.
KATHY030 wrote:What does library mean?
Libraries refers to the number of libraries the tag was found in. A library contains all of the gene's products (mRNAs) expressed in a given tissue. If there is a "2" under column B, that gene was found in both of the tumor libraries.
KATHY030 wrote:What does F and Q mean?
Increasing F, or decreasing Q, will increase the stringency of the search; the search will yield fewer genes, but their differential expression will be more statistically significant.
Q measures the "false discovery rate," which is the probability that sampling error, rather than real biology, accounts for the fact that a tag has been observed to occur more frequently in one library pool than in a second library pool. Low values of Q mean the difference is more likely to be real, and not caused by random chance. In other words, a low value of Q (< 0.01) means that there is a strong probability that the tag occurs more frequently (even only slightly more frequently) in one pool than in the other. Look for genes that have low values of Q when you pick genes for further analysis.
KATHY030 wrote:What are tag odds?
Tag Odds A:B is a number that reflects how significant the data are.
KATHY030 wrote:How do I know when a gene is overexpressed?
Scroll to the bottom of the list to find the genes that are over-expressed in cancer tissue (B>A, where B is the pool of genes from cancerous tissue and A is the pool of genes from normal tissue).
KATHY030 wrote:So if the pancreas in a cancer is red that means its over expressed??
Basically, yes. Here is how the project describes it: "Click on the picture of a body under SAGE Anatomic Viewer. You will see a table with data comparing expression of CLASP2 in a variety of normal and cancerous tissues. Below is a small section of this table showing pancreatic tissue, with red indicating over-expression. Note that CLASP2 over-expression is associated with pancreatic cancer, but not with other types of cancer."
Let us know if you have more questions.