Science Buddies: "Ask an Expert"

Hi,

I am doing the Cancer Genome Anatomy Project. I wanted to know what am I really able to test with SAGE Genie. Which questions regarding genes can be answered using SAGE Genie?

Hi Science1234,

Would you be able to provide more background on your project. The SAGE Genie is not a test. It is a software tool used to study gene expression (or how and when genes are turned into proteins).

Hi,

I am essentially trying to do the cancer genome anatomy project that is available on this website. But, I want to bring variations to it. Does anybody have any clue what I can add on or change in the cancer genome anatomy project that is available on science buddies? I need a few variations that I could do. Also, are the following questions answerable by SAGE Genie: what are over-exressed genes? what are the functions of over-expressed genes in cancer tissues? Also, can I use SAGE Genie to compare the over-expression of genes within different types of cancer, like colon and breast cancer? Lastly, what would be my hypothesis, variable, and control group for this experiment?



PLZZZZZZZ HELP OUT!!

Hi Science1234,

It's great that you're trying to do such an advanced project this early.

Researchers have found over the years that genes are not expressed normally in cancers as they are in normal tissues. For example, genes called growth factors (which allow cells to grow) are expressed in rather small amounts in normal tissues, but are highly expressed in cancers. This is an example of gene overexpression, when a gene makes more product than it normally should.

Yes, you can use SAGE genie to look at over-expressed genes. However, this subject has been pretty much beaten to death by researchers. It might be better to focus on one specific gene and see how that gene affects other proteins/genes (as most genes are part of a long pathway). If you still want to go forward with your current project, the control would be normal tissue from the colon or breast and your hypothesis would be that there is a difference in gene expression of certain genes between cancer and normal tissue.

My one concern is... Do you have access to a lab that will allow you to obtain cancer/normal tissue as well as the necessary chemicals and techniques?

Hope that helps!

-Sam

Hi,

Thanks for the quick reply Sam! Also, could you explain exactly what you mean by: It might be better to focus on one specific gene and see how that gene affects other proteins/genes (as most genes are part of a long pathway). Could you please use an example to explain, so that I can easily understand it. Also, does anyone have any clue as to which lab I can conduct my project at? Along with the lab, will there be any mentor that can assist me in my project? Lastly, does anyone have any input on how I can conduct this experiment (please provide step-by-step directions, PLZZZZ) for looking at one specific gene and seeing how that gene affects other proteins/genes? Could you please include in there the role of SAGE Genie.

THANKS!!!!!!

Hi - to help the Experts who may assist you with questions, here is the url for this project:
https://www.sciencebuddies.org/science- ... p011.shtml

The Cancer Genome Project on the Science Buddies site is a project you do using a bioinformatics tool and available data. You won't need to be in a lab setting for this project. The Experimental Procedure is designed to guide you through the process.

If you have questions about the steps of the Experimental Procedure, post back to this thread and the Ask an Expert team will help.

Good luck!
Amy
Science Buddies

Ok....... so what exactly are your inputs on how to do the Cancer Genome Anatomy Project on this website? Essentially, what can I add on/vary from the project available on science buddies? What would be my variable, control, and experimental group? What are some of the questions that I can form to conduct this experiment and use data from SAGE Genie as my project?????? Please also include the hypothesis!!!!!!!

Ok....... so what exactly are your inputs on how to do the Cancer Genome Anatomy Project on this website? Essentially, what can I add on/vary from the project available on science buddies? What would be my variable, control, and experimental group? What are some of the questions that I can form to conduct this experiment and use data from SAGE Genie as my project?????? Please also include the hypothesis!!!!!!!


PLEASE REPLY ASAP!!!!!!!!

I really need your help!!!!! Why isn't anyone replying to my questions????????????


PLEASE HELP OUT!!!!!

Hi there,

The experts on this forum do not necessarily check the forum every day, which may be why there has been some delay in responding to your questions. Also, we are here to help you develop and improve your project, but not to hand you a hypothesis. You will get the best experience out of your project if you come up with your own hypothesis, based on some background reading.

What interests you in the cancer genome project? Are you interested in what causes a certain type of cancer, or how cancer can spread to different tissues? If you have some specific questions that interest you, we can help you turn one of them into a workable hypothesis.

Heather

Ok....first off, here are my questions: What are over-expressed genes? What is the function of an over-expressed gene? Which genes tend to be more over-expressed in certain types of cancer? I am focusing on lung and breast cancer (would it be a better idea to just focus on one cancer?) I need help with forming a hypothesis. Also, when I conduct my experiment, will SAGE Genie be able to answer the questions that I have formed? Lastly, could you please give examples of more "deeper" questions that SAGE GENIE can answer, other than the ones that I have!

Ok....first off, here are my questions: What are over-expressed genes? What is the function of an over-expressed gene? Which genes tend to be more over-expressed in certain types of cancer? I am focusing on lung and breast cancer (would it be a better idea to just focus on one cancer?) I need help with forming a hypothesis. Also, when I conduct my experiment, will SAGE Genie be able to answer the questions that I have formed? Lastly, could you please give examples of more "deeper" questions that SAGE GENIE can answer, other than the ones that I have!


Also, what are some ways that I can convert this demonstrative project into an experimental project?

PLEASE REPLY!!!! I NEED HELP BUT NO ONE HAS BEEN REPLYING!!!!!!!!

Hi there,

You have some very interesting questions. Over-expressed genes are genes that are normally not expressed very much (if at all) in a cell, but start to be expressed very highly in certain cells. It helps to understand that gene expression usually leads to the production of a protein. When a gene is over-expressed, there is a lot more of that protein in the cell than there should be.

You asked, "Which genes tend to be more over-expressed in certain types of cancer?" This is exactly the kind of question you can answer with the project you have chosen. Your hypothesis would be your prediction as to which genes might become overexpressed in lung or breast cancer. While it might be easier to focus on only one type of cancer, you could choose to see if there are any genes that are over-expressed in both types of cancer. (This might be a "deeper" question.) Another extension may be to look at what genes are involved in metastasis - the condition in which cancer spreads to other tissues.

I hope this helps!

Heather

So......by using sage genie to answer the question: which genes tend to be more over-expressed in certain types of cancers or two types of cancers? would that make my project an experimental project and not just a demonstrative one? Also, how can i go along testing which genes are over-expressed in metastasis? Can sage genie provide an answer to that question?? Could you please provide more info. on the thing about genes in metastasis!!!!!!!! PLZZZ!!!! Also, what are some examples of genes that could be over-expressed in both lung and breast cancer? What would be their functions?

Hi,

Using SAGE GENIE to discover which genes are over-expressed in certain kinds of cancer may be considered experimental, but you should check with your teacher to be sure.

I am not sure how to use SAGE GENIE to detect metastasis. It was a suggestion you could explore further if you were interested.

Since this is not my particular area of expertise, I don't have examples of genes that would be over-expressed in certain cancers. The point of your experiment is to find out! If you want to come up with hypotheses, you should use your background research to help you with that.

Good luck!
Heather

Could someone who is an expert in the cancer genome anatomy project please respond to my following question: which genes are over-expressed in both lung cancer and breast cancer and what is their function? I have done background information, but no source gives the name of the genes.......!!!!!! Also, how can SAGE Genie be used to detect metastasis????????? PLEASE RESPOND ASAP!!!!!!!

Ok.....it has been a while and no one is responding!!!!!!!! Is it possible to use sage genie to detect under expressed genes in cancer cells? Could someone who is an expert in the cancer genome anatomy project please respond to my following question: which genes are over-expressed in both lung cancer and breast cancer and what is their function? I have done background information, but no source gives the name of the genes.......!!!!!! Also, how can SAGE Genie be used to detect metastasis????????? PLEASE RESPOND ASAP!!!!!!!

Hi there,

I'm sorry that no one else has been responding to your posts. As I said, this is not my area of expertise, so I have answered your questions the best I can.

I really think you need to start using SAGE Genie to find out which genes may be overexpressed in lung and breast cancer. Have you tried exploring the program to see if any candidate genes arise?

Hopefully someone more familiar with SAGE Genie and/or cancer can chime in...

Good luck!
Heather

Hi Heather,

Thanks for your quick reply. I actually did run the Sage Genie test for only breast cancer, and all the genes were under-expressed, none were over-expressed? Also, I would like to know that would this project be considered experimental (using sage genie to find out the over-expressed/under-expressed genes in certain type(s) of cancer(s) and predict their involvement with cancer cells? Please reply asap!

okay.....i HAVE NOT GOTTEN A REPLY IN MONTHS...literally!!!!!!! could someone at least reply to this post!!!!!!!!! okay......so....i ran the sage genie test for brain cancer and i am looking at over expressed genes....do u think the following questions are answerable based on the results of running sage genie: what is the function of over-expressed in brain cancer tissues and which genes tend to be more over-expressed in brain cancer tissues? are there any other questions that are answerable by running the sage genie software and collating data????


PLEASE REPLY ASAP!!!!!!!! PPPPPLLLLLEEEEAAASSSSEEE!!!!!

Hi Science1234,

I understand your frustration, but I noticed that you also have multiple threads for this same topic, which makes it more difficult for the Experts to follow your line of questioning and your project details.

As I mentioned previously, this is not my area of expertise. However, it looks as if you have made some progress by finding some genes that are overexpressed in brain cancer. Based on what you've said, you have answered the question of which genes tend to be overepxressed in brain cancer tissues. You will need to do some research, but should be able to find out the functions of the genes that are overexpressed in brain cancer. If you find out their functions, you may be able to come up with some ideas as to why their overexpression could lead to tumor formation. This would likely be enough for your project.

If you are determined to take things further, another question you could ask is what genes may be overexpressed in multiple cancer types.

I hope that helps you continue to make progress.

Good luck,
Heather

Hi Heather,

THANKS SO MUCH!!! also, i only have one thread...this one! the other ones are not mine....also, are all the questions that i posted on the previous thread able to be answered by the SAGE GENIE data??? also, is this project considered experimental??

Hi Science1234,

If you have access to journal articles (ie being part of some larger institution), you can look for PubMed articles related to the genes you are looking for (just search for papers with the gene name) and you can also look up the gene on the gene site on PubMed to look at its function and type of protein.

Hope that helps!

-Sam

Hi Science1234,

You can definitely use Sage Genie to answer the questions of which genes are overexpressed or underexpressed in certain types of cancer. To figure out the functions of those genes, you will need to do research outside of Sage Genie (including scientific journal articles, as Sam suggested).

I'm not sure whether Sage Genie can be used to investigate metastasis. That is an extension question that might require capabilities outside those of Sage Genie.

Some might consider your project experimental, if you come up with a hypothesis and test it using Sage Genie. Others may not, because you are not doing the actual testing; you are just using a resource. You will need to ask your teacher whether he/she thinks this project will satisfy the requirement that you do an "experiemental" project.

Hope that helps...

Heather