CANCER GENOME ANATOMY PROJECT

[KATHY030]

I REALLY NEED HELP PLEASE

I'm doing the cancer genome anatomy project and I am doing my research paper and I need to state my hypothesis for my project. I tried to find a hypothesis but I can't seem to find one. Can someone please help me find a hypothesis for this project, its urgent my research paper is due tommorow. PLEASSE HELP.

[donnahardy2]

Hi,

I think this is the project you are doing and it is a really great project.

https://www.sciencebuddies.org/science- ... p011.shtml

In this project you will be comparing the expression of genes in normal and cancer tissue, so you are looking for genes with higher expression levels compared to normal tissue.

Here is the information on the science buddies website for writing your hypothesis:

https://www.sciencebuddies.org/science- ... esis.shtml

You can state your hypothesis something like: “if I compare gene expression in normal and cancer tissue, there will be a higher level of expression in cancer tissue.” And you can be more specific if you are looking at specific genes or types of cancer.

I hope this helps.


Donna Hardy

[KATHY030]

Hi I'm doing the CANCER GENOME ANATOMY PROJECT but I don't get the point of the project what Am I suppose to find out.
Plus I've tried like a millions of times to make a hypothesis; I got help but I still didn't understand, the science buddies page for this project states in one of the steps to "17.Can you hypothesize what functions the over-expressed genes might have in cancer cells? This is how some cancer research projects in university and biotechnology labs are launched!" Can someone please help me make a hypothesis because I'm just lost in this project I really don't get it. Plus i variations it also saids Can you identify genes that are over- or under-expressed in more than one type of cancer? Can you make a case for why a particular gene is over-expressed? Put your ideas in the form of a hypothesis.Please help me make a hypothesis it's urgent.
I also need help what does this mean [ A > B ] [ A < B ] ?
What is a tag I din't understand that?
What does library mean?
What does F and Q mean?
What are tag odds?
How do I know when a gene is overexpressed?
So if the pancreas in a cancer is red that means its over expressed??

PLEASE HELP ME IM JUST LOST, I DON't GET IT

[KATHY030]

CAN someone please answer my questions please

[deleted-71536]

Hi Kathy,

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.

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.

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.

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.

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.

What are tag odds?

Tag Odds A:B is a number that reflects how significant the data are.

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).

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.

Good luck,
Heather

[deleted-177207]

I am doing this great project but Ia m a Lil Bit concerned because i need help in the step # 13 what table # wHaT TABLE IS THAt...pLEASEEEEE HElP MY PROJECT IS DUE FOR 21 and today is 17

[deleted-71536]

Hi Paola203,

It is hard to tell from your post whether you are doing the Cancer Genome Anatomy Project (https://www.sciencebuddies.org/science- ... p011.shtml) or something entirely different. If you are doing the Cancer Genome Anatomy Project, step #13 of the procedure (https://www.sciencebuddies.org/science- ... #procedure) shows a table with data about the expression of the CLASP2 gene. In this case, the gene has bigger numbers in column B (pancreatic cells with cancer) than column A (normal pancreatic cells). This says that the CLASP2 gene is overexpressed in cancer cells.

If you want to do this project, I recommend following the procedure step-by-step to understand how the program works, and then you can try it with different genes.

If you are not doing the Cancer Genome Anatomy Project, please tell us more about what you are doing so we can help you.

Heather

[deleted-177207]

Hii!!!

Yep I am doing this project step by step nothing different....
MY Hypothesis is "If I compare gene expression in a normal pancreas and in a cancer tissue,in the cancer tissues I find a higher level of over-expressed genes"
but I need THE STEP 13 links where said the genes over-express in am in a big rush right NOW BECAUSE WITH THOSE LINKS I made the conclusion of my science fair but I need the names of the over expressed genes...
I understand everything in ths project except the step 13
PLEASE HELP ME
If you can give me the link of step 13 i'd appreciate it
LEASE ANSWER

[deleted-71536]

Hi Paola203,

The link in Step 13 is not in the Science Buddies procedure, but rather in the program itself. If you have been following the procedure step-by-step in the SAGE Genie program (http://cgap.nci.nih.gov/), then you will have the capability to click on different overexpressed genes. If you are having trouble finding the link, try clicking it in Step 10 (before you explore the Tag link and the Anatomical Viewer).

The point of Step 13 is to give you more information about the particular gene (CLASP2, in this case). You will want to repeat the procedure for other genes to test your hypothesis. Remember that, in science, we do not manipulate the data to fit our hypothesis, but instead base our conclusions on the data. So you need to complete the procedures to make sure that your conclusions fit with the data (not the other way around).

I don't have a way to send you the link in Step 13. You need to work through the program yourself (with multiple genes) to complete the project. As I said before, try getting to the link the first time you see the data in Table 2, and see if that helps.

Let me know if you are still having trouble.

Heather

[deleted-177207]

Okey thats means the CLASP2 is a gene over-expressed so i cant made a conclusion with that because i only need one gene over expressed..
I dont need more but the question is I can find more information aboout this gene in the page or i need to find in the internet?


the problem is i dont find that genes CLASP2 OR ANY OTHER WITCH NUMBER FOUND 3619
AND THE PROBLEM IS DUE FOR 21 I AM STOCK AND IS MY FIRST SCIENCE FAIR AND BY THE WAY IN ENGLISH I BE HERE 5 MOTHS in moments like this i want to go home GOD

[deleted-71536]

If I compare gene expression in a normal pancreas and in a cancer tissue,in the cancer tissues I find a higher level of over-expressed genes

Based on this hypothesis, I think you need to find more than one over-expressed gene, since some genes may be under-expressed. Otherwise, this is a circular argument, since the definition of the genes being over-expressed is that they are found at higher levels.

You can find more information about the gene in the SAGE Genie program itself.

Heather

[deleted-177207]

how I know what are the over expressed genes i know is too late but a need one more over expressed genes what are the characteristic

[deleted-71536]

Hi Paola203,

The simplest way to understand it is that Pool A represents normal tissues, and Pool B represents cancerous tissues. If you see bigger numbers in column B, then that gene is overexpressed in cancer cells (compared to normal cells). If you see bigger numbers in column A, then that gene is underexpressed in cancer cells.

Heather

[Medical-stuff]

Hi Paola203,

The simplest way to understand it is that Pool A represents normal tissues, and Pool B represents cancerous tissues. If you see bigger numbers in column B, then that gene is overexpressed in cancer cells (compared to normal cells). If you see bigger numbers in column A, then that gene is underexpressed in cancer cells.

Heather

Hi I have two questions:
Why is it taking so long for the Cancer Genome Anatomy Project website to Email me my information?!
Also.......
How do you do the hypothesis for the cancer genome anatomy project ????

[Medical-stuff]

Is anybody there?!!?!!!!!?!????this is serious I only have 2 weeks to complete this so I need help NOW!(not being harsh or anything though...)

[deleted-71536]

Hi Medical-stuff,

Welcome to Science Buddies! Because each Expert usually checks the forums once a week, it typically takes 1-2 days to get a response to a post. Also, you posted in an existing thread, which did not alert Experts that you were a new user with new questions.

Why is it taking so long for the Cancer Genome Anatomy Project website to Email me my information?!

I am not sure what you are expecting to see via e-mail. You can perform this project online through a website: http://cgap.nci.nih.gov/

How do you do the hypothesis for the cancer genome anatomy project ????

If you scroll up to earlier in this thread, you will see that Donna Hardy answered a similar question about the hypothesis for this project:

In this project you will be comparing the expression of genes in normal and cancer tissue, so you are looking for genes with higher expression levels compared to normal tissue.

Here is the information on the science buddies website for writing your hypothesis:

https://www.sciencebuddies.org/science- ... esis.shtml

You can state your hypothesis something like: “if I compare gene expression in normal and cancer tissue, there will be a higher level of expression in cancer tissue.” And you can be more specific if you are looking at specific genes or types of cancer.

I hope this helps. Please post again (in this same thread) if you have more questions.

Heather

[Medical-stuff]

Here is the information on the science buddies website for writing your hypothesis:

https://www.sciencebuddies.org/science- ... esis.shtml

You can state your hypothesis something like: “if I compare gene expression in normal and cancer tissue, there will be a higher level of expression in cancer tissue.” And you can be more specific if you are looking at specific genes or types of cancer. [/quote]

Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?!
That's the part I don't get!

[deleted-71536]

Hi Medical-stuff,

Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?!
That's the part I don't get!

It really depends on the gene. The problem with cancer cells is that they grow out of control. There could be an overexpression of genes associated with cell division, or there could be an underexpression of genes meant to stop cell division when space is limited. You can start by focusing on a single gene, and see whether that gene is overexpressed or underexpressed in cancer cells compared to normal cells.

Note that you are not causing the expression to happen. You are looking at what has already happened. So when you ask, "Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?" the answer is yes (for overexpressed genes). That higher expression is exactly what you are measuring. Then you can look at what gene is being overexpressed in cancer cells, and see why that might cause cancer.

Heather

[Medical-stuff]

Hi Medical-stuff,

Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?!
That's the part I don't get!

It really depends on the gene. The problem with cancer cells is that they grow out of control. There could be an overexpression of genes associated with cell division, or there could be an underexpression of genes meant to stop cell division when space is limited. You can start by focusing on a single gene, and see whether that gene is overexpressed or underexpressed in cancer cells compared to normal cells.

Note that you are not causing the expression to happen. You are looking at what has already happened. So when you ask, "Wouldn't cancer tissues ALREADY have a higher expression over normal tissues?" the answer is yes (for overexpressed genes). That higher expression is exactly what you are measuring. Then you can look at what gene is being overexpressed in cancer cells, and see why that might cause cancer.

Heather

So do you think that I should predict which two cancers I think will have similar genes that are over expressed for my hypothesis?

[deleted-71536]

Hi Medical-stuff,

Your exact hypothesis is really up to you. If you would like to compare two different cancers, that sounds like an interesting project. You can also see whether two different cancers have overexpression in the same organs.

Good luck!

Heather

[Medical-stuff]

Hi Medical-stuff,

Your exact hypothesis is really up to you. If you would like to compare two different cancers, that sounds like an interesting project. You can also see whether two different cancers have overexpression in the same organs.

Good luck!

Heather

What do you mean "having an over expression in the SAME organ"?!
=_=?!

[Medical-stuff]

Hi Medical-stuff,

Your exact hypothesis is really up to you. If you would like to compare two different cancers, that sounds like an interesting project. You can also see whether two different cancers have overexpression in the same organs.

Good luck!

Heather

What do you mean "having an over expression in the SAME organ"?!
=_=?!

Please help me?!!!!!!!!!!i am doing hypothesis and materials and Procwdure TODAY so I really need a reply before 9:00pm!!!
PLEASE!!!

[deleted-81235]

Heather is given you some great advice and suggestions, and only she can really explain what she meant by that, but I think that she meant that instead of comparing overexpression of genes in different cancers, you might want to consider comparing whether or not the same genes are overexpressed in cancer in the same organ. I think the part that you are misunderstanding is that there is no one type of cancer in an organ. Lung cancer is a general term used to describe many different forms of cancer. Cancer at its simplest is an uncontrolled overgrowth of one type of cell, and since the lung is made up of many different types of cells, there can be many different forms of cancer. Cells are different because each type has a unique purpose, and they all work together to form a functioning organ. Each different type of cell, if it becomes cancerous, causes a different type of cancer (because the cells that cause them are different). Take for example, bronchioalviolar cell carcinoma and squamous cell carcinoma. Both of them occur in the lungs, but bronchioalviolar cell carcinoma occurs in the bronchial cells, while squamous cell carcinoma occurs in squamous cells. So, what I think that Heather was trying to suggest is that you compare the different genes that are overexpressed in two different cancers (bronchioalviolar cell carcinoma and squamous cell carcinoma) that occur in the same organ (lung).

I just want to add that Heather, and all of the other experts, can't always respond before your deadlines because this is not our job, and no one asked us to do this. We all volunteer our time to help you, and all we ask for is a little patience in return. I hope you understand.

Thanks, and I hope I helped!

Meg

[Medical-stuff]

Heather is given you some great advice and suggestions, and only she can really explain what she meant by that, but I think that she meant that instead of comparing overexpression of genes in different cancers, you might want to consider comparing whether or not the same genes are overexpressed in cancer in the same organ. I think the part that you are misunderstanding is that there is no one type of cancer in an organ. Lung cancer is a general term used to describe many different forms of cancer. Cancer at its simplest is an uncontrolled overgrowth of one type of cell, and since the lung is made up of many different types of cells, there can be many different forms of cancer. Cells are different because each type has a unique purpose, and they all work together to form a functioning organ. Each different type of cell, if it becomes cancerous, causes a different type of cancer (because the cells that cause them are different). Take for example, bronchioalviolar cell carcinoma and squamous cell carcinoma. Both of them occur in the lungs, but bronchioalviolar cell carcinoma occurs in the bronchial cells, while squamous cell carcinoma occurs in squamous cells. So, what I think that Heather was trying to suggest is that you compare the different genes that are overexpressed in two different cancers (bronchioalviolar cell carcinoma and squamous cell carcinoma) that occur in the same organ (lung).

I just want to add that Heather, and all of the other experts, can't always respond before your deadlines because this is not our job, and no one asked us to do this. We all volunteer our time to help you, and all we ask for is a little patience in return. I hope you understand.

Thanks, and I hope I helped!

Meg

Thank you thank you thank you thank you!!!!you cleared up all my questions&had a very descriptive answer!!!!!but I have just one more question:how can I use the cancer genome anatomy project website for THAT cell?
Science buddies only gives me the way of how to use the website for pancreas cancer.....

[deleted-71536]

Thanks, Meg, for stepping in while I was away.

I have just one more question:how can I use the cancer genome anatomy project website for THAT cell?
Science buddies only gives me the way of how to use the website for pancreas cancer.....

The Science Buddies website gives you an example using the pancreas, but the Cancer Genome Anatomy Project website (http://cgap.nci.nih.gov/) allows you to compare the expression of genes for the same cancer in different organs, or to compare different types of cancer in the same organ.

Have you tried playing around on the website yet? I think that it will help for you to check out how the website works and try different things. In fact, playing around with different cancers, different organs, or different genes, might lead you to come up with a new hypothesis! Usually scientists base their hypotheses on their own observations, and then do an experiment to see whether their hypothesis is supported by the data. I suggest that you try out the website and see what you can do with it. Then we can help you hone your particular hypothesis and interpret the data you collect.

Cheers,
Heather

[Medical-stuff]

Yes I have done that but I think I'm
Going to do what science buddies procedure is and improvise from that because I don't have a lot if time to finish I have about 1 or 2 weeks
Thank you so so so so so so much!!!!I'll come back with more questions later like graphing and result things...yah stuff like that.Bye:);)I'll be back!!!

[deleted-71536]

No problem. Glad you have a direction. Looking forward to your updates as the project progresses.

Heather

[Medical-stuff]

I am still waiting for the cancer genome anayomy project website to send me my email!
It's taking FOREVER!:D
It usually comes at 9:12pm but I may come and ask questions at like 9:30-10
(Just to let you know!):);)

[Medical-stuff]

Ok so does it have to be red in the normal part to be cancerous or does it have to be ok the cancer
Side and be red?-the cancer genome anatomy project

[Medical-stuff]

Hi
Ok so for my hypothesis for the cancer genome anatomy project I have just learned that pancreas and stomach cancer have the most common over expressed genes

Now what I really need help is on creating a hypothesis for THAT!!!