CANCER GENOME ANATOMY PROJECT

deleted-81235 · Post by **deleted-81235** » Sun Feb 17, 2013 1:09 pm

It really depends on what your teacher wants. Definately write your hypothesis so it's understandable. My teacher always said to write an "if-then-because" statement as my hypothesis. The 'because' part explains why you think the 'then' part of the statement (the results) will occur. That would be my advice, but you might want to wait for Heather to return to your thread because she knows a lot more about your experiment than I do.

I hope this helps!
Meg

Medical-stuff · Post by **Medical-stuff** » Sun Feb 17, 2013 1:23 pm

Ummm I said that my independent variable would be the over expression in the bred in the pancreas and liver BECAUSE the level of expression will be changing and the ore expressed the fee is in cancer the more likely IT IS TO BE A CANCER CELL?
The capatalized part is the part I am unsure of.
Please help.

deleted-71536 · Post by **deleted-71536** » Mon Feb 18, 2013 2:45 pm

Hi Medical-stuff,

Sorry for the delay in my response. Let's start with your hypothesis.

If you use this version...

heatherL wrote:"I hypothesize that since the pancreas and the liver have similar jobs of sending digestive substances to the duodenum they will also have similar genes that are overexpressed when cancer develops."

...then you could say that "IF you compare gene expression in pancreatic and liver cancer, THEN you will see overexpression of similar genes when cancer develops BECAUSE the pancreas and the liver have similar jobs of sending digestive substances to the duodenum." Is that the format your teacher wants to see?

Medical-stuff wrote:Also for hypothesis I don't really know what my controlled variable,independent and dependent variables would be.

Your independent variable is the one that you change in the experiment. In this case, it is the presence or absence of cancer. (You are not really changing this yourself, but it is what you are comparing.) Your dependent variable is the one you measure, because it is dependent on the variable you're changing. In this case, your dependent variable is the amount of gene expression. It's hard to pinpoint a controlled variable for this experiment, since you're really doing it on the computer, but you are only looking at pancreatic and liver cancer, so I suppose the type of cancer could be your controlled variable.

Here is more information about variables:
https://www.sciencebuddies.org/science- ... bles.shtml
https://www.sciencebuddies.org/science- ... bles.shtml

Medical-stuff wrote:For my data would I make graphs showing a gene and how much it is overexpressed in cancer compared to it being under expressed in a normal body?

For your data you will probably make a graph showing which genes are overexpressed in pancreatic cancer, which ones are overexpressed in liver cancer, and which ones are overexpressed in both types of cancer. You won't be able to tell how much the genes are overexpressed; you can only tell if they are overexpressed or not.

Medical-stuff wrote:Also for my research really what you are telling me is that I need to explain my project like tell about pancreas ,functions,pancreas cancer & lung,functions,lung cancer
And should my research paper have like after I finish my actual RESEARCH behind it ,for example,a paper telling materials used,then procedure,etc.?

Your research paper should provide the relevant background for the experiment you are doing. Information about the pancreas, liver, and how cancers develop are good topics for your research paper. The Science Buddies information (https://www.sciencebuddies.org/science- ... aper.shtml) is a wonderful resource and will walk you through the process step-by-step.

Best,
Heather

Medical-stuff · Post by **Medical-stuff** » Mon Feb 18, 2013 6:35 pm

Ummmm ok could you explain how I would do my data please a little more?
And also can you explain to me how to do the conclusion?

deleted-71536 · Post by **deleted-71536** » Tue Feb 19, 2013 7:44 pm

Hi Medical-stuff,

Your best strategy is to follow the procedure as laid out on the Science Buddies website: https://www.sciencebuddies.org/science- ... #procedure

Start by figuring out which genes are overexpressed in pancreatic cancer. Then see if you can find out the functions of those genes. Next, do the same procedure for liver cancer. Do you see similar genes overexpressed in both types of cancer? If so, what functions do they have?

Once you have answered these questions, we can talk about the conclusions you can make.

Best,
Heather

Medical-stuff · Post by **Medical-stuff** » Wed Feb 20, 2013 4:49 am

Ok I'll do that today then we can do graphs.
It is very important that you are here today(Wednesday) and tomorrow(thursday) because my science fair is due Friday!

deleted-71536 · Post by **deleted-71536** » Wed Feb 20, 2013 11:45 am

Hi Medical-stuff,

I am teaching classes today and tomorrow, but I will do my best to respond. The other experts can also help you with data presentation and interpretation, and Science Buddies has even more resources about those topics:
Data Analysis & Graphs: https://www.sciencebuddies.org/science- ... ysis.shtml
Conclusions: https://www.sciencebuddies.org/science- ... ions.shtml
Sample Conclusions: https://www.sciencebuddies.org/science- ... ions.shtml
More about Conclusions: https://www.sciencebuddies.org/science- ... usions.pdf

Heather

Medical-stuff · Post by **Medical-stuff** » Wed Feb 20, 2013 11:22 pm

Hi ok so the cancer genome anatomy project website isn't working it isn't sending me my email!!!this is due tomorrow!!! Please HELP!!!!!!!!!!!!!

Medical-stuff · Post by **Medical-stuff** » Thu Feb 21, 2013 2:13 am

Ok so far for the research paper I wrote: where the liver and pancreas is
What their functions are
And about pancreas and liver cancer(2 paragraphs per bullet point)
(ex.)1 paragraph is about pancreas then the next about liver)
Now I'm gonna add two more paragraphs about how those cancers are treated then I will go back to my beginning of my research paper and add how cancer is formedade in blood.
I found a really good site that explained how it forms and it is very nice

So, so far I have
Question(also about my question, I have seemed to have lost what I am actually asking would it be "what two organs will have similar genes when over expressed?")
Hypothesis
Research(almost done)
I'm going to do materials and procedure at Lunch
Then I will finish by doing data(which I still need a little help on)
TODAY IS THE LAST DAY I CAN WORK ON THIS!

-I'll keep you posted.

Medical-stuff · Post by **Medical-stuff** » Thu Feb 21, 2013 6:24 pm

Hi heather!! Ok well here's the situation I'm still having trouble with how to make the data graphs but everything else is pretty much ok also I need you to hear my hypothesis paragraph please!
Please respond soon ,today..it's my last day of working on this project!

Medical-stuff · Post by **Medical-stuff** » Thu Feb 21, 2013 11:10 pm

HELPPPPPPPPPP
I HAVE ALL MY INFORMATION I JUST DON'T KNOW HOW I AM SUPPOST TO MAKE IT INTO GRAPHS!!!!!!!!!ugh help!!!!!!

deleted-71536 · Post by **deleted-71536** » Fri Feb 22, 2013 7:31 am

Hi Medical-stuff,

As I said, I am teaching today, but I will try to help you. I cannot give you any feedback if you do not tell me what you have. Please upload your information as an attachment or list it directly in the forum so I can review it.

Heather

Medical-stuff · Post by **Medical-stuff** » Fri Feb 22, 2013 2:36 pm

Ok I'll send it To you. I did not turn in it today do I am turning it in Monday

Medical-stuff · Post by **Medical-stuff** » Sat Feb 23, 2013 11:08 am

Ok I attached what I have done so far.
I didn't put my materials and procedure in the attachment.
it includes my question(is it correct?)
hypothesis
research paper
and i'll add my graphs in another post...

Medical-stuff · Post by **Medical-stuff** » Sat Feb 23, 2013 11:09 am

also do you think I should add more to my research paper? I can
There is one kid who had 30 pages for his reserch paper. I mean I could do that but I know I still need to add a little more to it.

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?

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