CANCER GENOME ANATOMY PROJECT

Medical-stuff · Post by **Medical-stuff** » Sat Feb 23, 2013 11:13 am

I'M GOING TO SEND YOU A PICTURE OF WHAT THE RUBRIC SAYS IS REQUIRED FOR THE PROJECT. aLSO i WILL SEND MY GRAPHS AND i WILL EXPLAIN WHAT THEY MEAN, BUT i KNOW FOR A FACT THAT I HAVE DONE THE GRAPHS WRONG BECAUSE I DIDN'T KNOW HOW TO DO THAT PART.

Medical-stuff · Post by **Medical-stuff** » Sat Feb 23, 2013 12:14 pm

Pictures:

Medical-stuff · Post by **Medical-stuff** » Sat Feb 23, 2013 12:24 pm

ok so I have now sent you all of my work

deleted-71536 · Post by **deleted-71536** » Sat Feb 23, 2013 3:43 pm

Hi Medical-stuff,

I did a quick read through your paper. You wrote the question, "What two organs will have similar genes when overexpressed in cancer?" I don't think that is what you are asking, since you only compared two organs. Instead, I think you are asking, "Will two organs of similar function have similar gene expression associated with cancer?"

Although it is very interesting, I do not understand why you included information about blood cells in your research paper. This would be relevant information if you did your project on leukemia (blood cancer), but you did not. I think it is best for you to focus on information about cancer in general, how certain genes can be linked to cancer, and finally the liver and pancreas.

Keep in mind that length alone is not important for your research paper. What is important is that your research paper provides the relevant background information for your project.

One important thing you should do (if you are able to, with your limited time left) is try to understand the function of at least some of the genes that are overexpressed in both liver and pancreas cancer. I know I suggested this earlier, and it will help you to interpret your data.

Does the table in your paper represent all of your data? It looks like you are only showing the genes which are overexpressed in liver and/or pancreas cancer. I think they have more overexpressed genes in common compared to the genes overexpressed in only one organ or the other. That is the kind of information that will help answer your original research question. In other words, answer these questions (with numbers): 1) How many genes are overexpressed in liver cancer? 2) How many genes are overexpressed in pancreatic cancer? 3) How many genes are overexpressed in both cancers? If the answer to #3 is more than half as big as #1 or #2, then the two cancers have similar gene overexpression.

I hope this helps. I am not on my computer all the time, so you will have to do your best on your own if I am not able to provide you more feedback before Monday. It looks like you are on your way, and I wish you the best with your project. Please let me know how it goes.

Heather

Medical-stuff · Post by **Medical-stuff** » Sat Feb 23, 2013 4:08 pm

Ok so I did do the part where you told me to find the functions of the genes and at theist they told me that for example:
ATGTGAAGAG. (over expressed in pancreas and liver) is secreted protein acid;cysteine rich

That's the type of info they tell me about the genes.

How many genes do you want me to test?
(I only tested 20)

Also the answer to your question #3 :
The genes I tested found that there was LESS genes that were similar for over expression in both cancers
In my case:
Pancreatic cancer : 18 genes over expressed. 2 under expressed
Liver cancer: 12 genes over expressed 8 under expressed
Similarities (both liver and pancreas): 10 genes over expressed. 10 under expressed

Do you see my problem?

Medical-stuff · Post by **Medical-stuff** » Sat Feb 23, 2013 4:21 pm

They have less genes that are over expressed in both.
So what I'm saying is that when u said that there should be more genes in common rather than overexpressed in only one organ or the other I got the complete opposite.
More genes were over expressed in one organ or the other rather than in both but I also think that my graphs aren't that clear. Can you help me?

I think they have more overexpressed genes in common compared to the genes overexpressed in only one organ or the other. That is the kind of information that will help answer your original research question.

deleted-71536 · Post by **deleted-71536** » Mon Feb 25, 2013 5:53 am

Hi Medical-stuff,

Sorry but I was not able to log onto the forum until this morning.

I did find your graphs confusing, and I think I know why. Your initial pie charts showing overexpressed vs. normally expressed genes in each organ are fine. When you are looking for overlap, you should only look at the overexpressed genes. For example, the liver had 12 overexpressed genes and the pancreas had 18. Out of those, 10 of the genes were in common. That means more than half of the overexpressed genes you found were shared (10/12 in the liver, 10/18 in the pancreas). So it looks like your hypothesis is supported by the data. You could try doing a Venn diagram (http://en.wikipedia.org/wiki/Venn_diagram) for the overexpressed genes only.

Your results may have been more striking if you had been able to look at more than 20 genes, but I still think you found something interesting to discuss.

You can beef up your conclusions by seeing whether any of the shared overexpressed genes are related to digestive functions (sending substances to the duodenum).

I hope this helps. Please let me know how everything turns out!

Best,
Heather

Medical-stuff · Post by **Medical-stuff** » Mon Feb 25, 2013 2:49 pm

Hi any last minute pice of advice?
I need help on graPhs!!!what type should I do then???
Today I'd last day my science teacher said I'm presenting tommorow!!!
Please help!!!

deleted-71536 · Post by **deleted-71536** » Mon Feb 25, 2013 7:09 pm

Hi Medical-stuff,

For your graphs, you can keep the pie graphs for the individual organ gene expression, and do a Venn diagram to show the overlap for the overexpressed genes.

I think your hypothesis was supported (at least with the genes you examined), but to really take it home I recommend looking up the functions of the overexpressed genes that the two organs had in common.

Best of luck with your presentation. Please let me know how it goes!

Heather

Medical-stuff · Post by **Medical-stuff** » Tue Feb 26, 2013 4:12 am

Ok I'll do that right now
I can do that!
Thanks!!

Medical-stuff · Post by **Medical-stuff** » Tue Feb 26, 2013 9:59 am

ok i did the venn diagram
i have 15 min left to work on it because im at lunch!!!!!!!!!!!!!
help me with the genes!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
i cant find any info on them!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

deleted-71536 · Post by **deleted-71536** » Tue Feb 26, 2013 11:29 am

Hi Medical-stuff,

It is probably too late at this point, so hopefully your presentation went well with the information you had. I think you ended up with a successful project, and hopefully you learned something in the process!

Best wishes,
Heather

Medical-stuff · Post by **Medical-stuff** » Tue Feb 26, 2013 4:39 pm

Hi ok so I'm last to present and luckily she told me I'm presenting tomorrow!!!so do I need an abstract?
And I'm also about to look at the genes functions for the similar ones.

deleted-71536 · Post by **deleted-71536** » Wed Feb 27, 2013 5:39 am

Hi Medical-stuff,

If you are doing a presentation board, it's often good to have an abstract. It's not usually a requirement, so your teacher is the best one to ask about that.

Let me know if you find out anything interesting about the gene functions.

I hope it all goes well!

Best,
Heather

Medical-stuff · Post by **Medical-stuff** » Tue Mar 05, 2013 4:44 pm

The genes that were similar mainly were PROTEIN MAKERS. Is that right?

deleted-71536 · Post by **deleted-71536** » Wed Mar 06, 2013 8:05 am

Hi Medical-stuff,

Yes, most genes code for proteins. The question is, what is the function of each protein? Are those proteins involved in the cell cycle, in chemical communication (hormones), or perhaps in the digestive functions of the organs you studied (liver and pancreas)?

Heather

Medical-stuff · Post by **Medical-stuff** » Mon Mar 18, 2013 6:37 pm

Hi heather!!!
I need help writing my purpose and abstract. I am not finding a lot if things to help write my purpose.
So far for my purpose:
The purpose of this project is to see if the pancreas and the liver will have the same genes that are over expressed when cancer develops. My reasoning for this was that I hypothesized that since both organs have similar functions in digestion, that they will have genes that had similar over expressed genes.

Medical-stuff · Post by **Medical-stuff** » Mon Mar 18, 2013 6:43 pm

Also *************************VERY IMPORTANT*************************
CAN I HAVE A LITTLE INFORMATION ABOUT YOU SO THAT I CAN ADD YOU TO MY ACKNOWLEDGEMENTS? please? tell me you name and other stuff. (better if you tell me the necessary components that I need to include for the acknowledgement)

I NEED YOU TO REPLY TO THIS AS SOON AS POSSIBLE!!!!!!!!!!!!!!! THE LAST DAY YOU CAN TELL ME THIS INFORMATION IS MARCH 19,2013!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
THANK YOU

Medical-stuff · Post by **Medical-stuff** » Mon Mar 18, 2013 6:45 pm

YOU COULD ALSO TELL ME WHAT TYPE OF PROFESSOR YOU ARE AT WHICH COLLEGE.(VERY HELPFUL)

deleted-71536 · Post by **deleted-71536** » Tue Mar 19, 2013 7:52 am

Hi Medical-stuff,

Medical-stuff wrote:I need help writing my purpose and abstract. I am not finding a lot if things to help write my purpose.
So far for my purpose:
The purpose of this project is to see if the pancreas and the liver will have the same genes that are over expressed when cancer develops. My reasoning for this was that I hypothesized that since both organs have similar functions in digestion, that they will have genes that had similar over expressed genes.

This is a good start. Maybe you could say something like this:

The purpose of this project was to examine gene expression associated with pancreas and liver cancer. I hypothesized that the pancreas and liver would have similar overexpression of genes with cancer because both organs have similar functions in digestion.

I appreciate you wanting to put me in the acknowledgements. I am happy for you to acknowledge me as Heather Liwanag from Science Buddies. I am an Assistant Professor of Biology at Adelphi University.

Good luck with your presentation!

Heather

Medical-stuff · Post by **Medical-stuff** » Tue Mar 19, 2013 3:40 pm

Hi heather, one last question that I really am not sure of:

1)when genes are over expressed in cancer, they are cancer cells.right?
2)when genes are under expressed in cancer, they are normal cells. Right?
3)when genes are over expressed in a normal body, they are normal cells. Right?
4)when genes are under expressed in a normal body, then what are they?

Also what is the exact definition of an over expressed gene and an under expressed gene?

deleted-71536 · Post by **deleted-71536** » Tue Mar 19, 2013 6:50 pm

Hi Medical-stuff,

The column identifies whether the cells are normal or cancerous. Some genes are expressed more in cancer cells, whereas other genes are "down-regulated," or expressed less in cancer cells. Everything is relative to a normal cell. So, to answer your questions...

Medical-stuff wrote:1)when genes are over expressed in cancer, they are cancer cells.right?

Yes, they are cancer cells because there is cancer present. In this case, the gene is expressed more than in normal cells.

Medical-stuff wrote:2)when genes are under expressed in cancer, they are normal cells. Right?

No. When genes are under-expressed in cancer, it means that the cell normally expresses that gene a lot more, but when cancer is present the gene gets turned off.

Medical-stuff wrote:3)when genes are over expressed in a normal body, they are normal cells. Right?

Yes, when genes are over-expressed in a normal cell, the cell is still normal. This is the other point of view for the situation described in question #2.

Medical-stuff wrote:4)when genes are under expressed in a normal body, then what are they?

They are normal cells. It just means that the gene is up-regulated (expressed more) when there is cancer. This is the other point of view for the situation in question #1.

To recap, the cells are labeled normal or cancerous based on whether cancer is present. Then, you compared gene expression. A gene that is over-expressed in cancer (under-expressed in normal cells) might be a gene that gets "turned on" when cells become cancerous, or might play a part in causing the cells to become cancerous. A gene that is under-expressed in cancer (over-expressed in normal cells) could be a gene that gets "turned off" when cells become cancerous.

I hope that clarifies things.

Heather

Medical-stuff · Post by **Medical-stuff** » Tue Mar 19, 2013 7:16 pm

Ok I understand this now but also what is the true meaning of "expression"?

deleted-71536 · Post by **deleted-71536** » Tue Mar 19, 2013 7:48 pm

Essentially, it's a way to describe how much protein is being made from that gene. More expression means more protein is being made. Less expression means less (or no) protein is being made.

Medical-stuff · Post by **Medical-stuff** » Tue Mar 19, 2013 8:04 pm

A gene that is under expressed in cancer(over expressed in normal cells) will not take part in creating cancerous cells.

correct???

Medical-stuff · Post by **Medical-stuff** » Tue Mar 19, 2013 8:17 pm

Expression- how much protein the gene is making. If it saying that the gene is over expressed then that means more proteins are being made. If it says that the gene is under expressed then that means less to no proteins are being made.

You will first try to see if the cell is cancerous or not depending on the cancer. After you complete that step, you will then compare the gene expressions.
A gene that is over expressed in cancer (under expressed in normal cells) means that it is a gene that will take part in making cells cancerous. A gene that is under expressed in cancer(over expressed in normal cells) will not take part in creating cancerous cells.

1)When genes are over expressed in cancer, they are cancer cells meaning cancer is present.
2)When genes are under expressed in cancer, it still expresses a gene a lot but will not be in use when cancer is present. It will "turn off."
3)When genes are over expressed in a normal body, it is a normal cell.
4)When genes are under expressed in a normal body, it is a normal cell that is expressed more when cancer is present.

i just typed this, is it correct?????????????????????????????????????/

deleted-71536 · Post by **deleted-71536** » Thu Mar 21, 2013 9:16 am

Hi Medical-stuff,

Sorry for the delay. I hope my response is not too late.

Medical-stuff wrote:A gene that is over expressed in cancer (under expressed in normal cells) means that it is a gene that will take part in making cells cancerous. A gene that is under expressed in cancer(over expressed in normal cells) will not take part in creating cancerous cells.

This is partially true. A gene that is over-expressed in cancer may play a role in making the cells cancerous. You can't tell whether the over-expression caused the cancer, or the cancer caused the gene to over-express. (That's why it helps to look at the function of the gene.) It is also possible that "turning off" a gene could cause cancer. For example, there are proteins involved in apoptosis (programmed cell death) that are expressed when the cell does not have the room or resources to keep growing and reproducing. Turning off those proteins could allow cancer to develop, since cancer cells continue to grow where they shouldn't.

Medical-stuff wrote:1)When genes are over expressed in cancer, they are cancer cells meaning cancer is present.
2)When genes are under expressed in cancer, it still expresses a gene a lot but will not be in use when cancer is present. It will "turn off."
3)When genes are over expressed in a normal body, it is a normal cell.
4)When genes are under expressed in a normal body, it is a normal cell that is expressed more when cancer is present.

I think you may be confusing "genes" and "cells" here (at least in your wording). Let's combine your statements:

1) When genes are over-expressed in cancer (under-expressed in normal cells), the gene products are produced more in cancer cells compared to normal cells.
2) When genes are under-expressed in cancer (over-expressed in normal cells), the gene products are produced less (or not at all) compared to normal cells.

The above statements combine your four statements into one. Does that help alleviate your confusion?

Heather

Medical-stuff · Post by **Medical-stuff** » Sat Apr 06, 2013 12:57 pm

Hello Heather, may I receive your email addess?

Medical-stuff · Post by **Medical-stuff** » Sat Apr 06, 2013 1:02 pm

isn't it online?

deleted-71536 · Post by **deleted-71536** » Sat Apr 06, 2013 2:34 pm

Hi medical-stuff,

It is against Science Buddies policy to post personal information, including e-mail addresses, on the forums. But if you do a little research online, you can find the information you need.

Best,
Heather

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