Can I use microarray data for signaling pathway analysis in cancer cell ?

Question

[waltwu512]

Hello, everyone.

Can I use microarray data for signaling pathway analysis in cancer cell? For example, compare normal and tumor tissue microarray data to find deferentially expressed genes, and then put them into DAVID or GO to check which "signaling" pathway(s) they are involved in. I know that signaling pathway is based on post-transcriptional modification. But I believe that the gene of some members involved in certain signaling pathway should be turn on if the certain signaling pathway is on, hence I can get some useful information about signaling pathway from microarray data. I just wonder why almost no articles are talking about using microarray data for "signaling" pathway analysis. Is my concept incorrect ? Or actually there are some related papers that I've missed ?

Many thanks.

Answer 1

[Devon Ryan]

If the pathways are altered at the transcript level then you certainly might be able to find them with a microarray. This isn't an uncommon thing to look for even. You'll typically see people just mention "pathways" rather than explicitly "signaling pathways".

[waltwu512]

Thanks for your answering.

Actually, I asked that because my project is focusing on "signaling" pathways. I think the range of the term "pathways" is wider than "signaling pathways". Most of "pathways" in articles including cell cycle, apoptosis, etc., the information of exact signaling pathways are relatedly not much. Could you please share a paper about signaling pathways analysis of microarray data?

[waltwu512]

I've found a paper about signaling pathways analysis of microarray data when I used pathways, microarray, and cancer as key word to search. There are some papers discuss signaling pathways indeed although most papers are not specifically talking about it.

Thanks for your help :)

[poulami2912]

Hi, I have a similar query and cannot find a relevant paper. Will you please share the paper?

Thank You

Answer 2

[ksuemail]

We have developed a powerful tool, OncoFinder. Our system takes gene expression data from your treated and control samples. By comparing to control samples, the OncoFinder calculates the pathway alteration of your treated samples.

We provide the analysis service for the research community for free and are looking for collaboration. Please send me a message if you are interested in the analysis.

[waltwu512]

Thanks for your answering.

That's sounds great. Is that an online software? Do you have papers about the OncoFinder?

In fact, I obtain microarray data from TCGA. If you are interested in the data, you can get the information from http://cancergenome.nih.gov/.

Last but not least, I am willing to collaborate if I have a chance. Can you tell me more details about your project?