Sources Of Information About Amplified Genes (And Overexpressed) In Cancer

Question

[Danielsbrewer]

I was wondering whether anyone could suggest sources of information about amplified genes in cancer, especially if the website tries to combine it with (over)expression information. We wrote a review on amplified and expressed genes recently and are trying to get a sense of what else is out there, so that when we update it we make sure we get different sources of information, not just a search of the literature.

[Malachi Griffith]

This tutorial describes several cancer data portals that might be relevant to this post: Exploring cancer mutation data portals

Answer 1

[Fred Fleche]

Web Resources To Find Cancer Indication Where A Given Gene Is Amplified

More over you can also try to correlate gene amplification and gene expression from the Sanger Tumor Cell Lines panel.

• Step 1: You can get the gene expression raw data here.
• Step 2: You can get some gene amplification data here]: [?]
• You display the CONAN web page for each human genes and get the cell lines where this genes is in a region with a copy number > 7 with a php script using regular expressions.

Update on October 21th 2010: Some amplification data from the Sanger Institute are available as an excel file (table of total copy number (cancer census genes and all cell lines used in analyses)) at this webpage

[Danielsbrewer]

Thanks for that. This suggests that there isn't that much out there at the moment.

Answer 2

[Danielsbrewer]

Here is a list of the sites I have found useful so far:

• CONAN
• Cancer Genome Workbench
• Breast
• Integrative Oncogenomics Cancer Browser - IntOGen
• Oncomine

Answer 3

[Nathan Harmston]

does something like COSMIC help you?

http://www.sanger.ac.uk/genetics/CGP/cosmic/

or some of the information from the Cancer Gene Census:

http://www.sanger.ac.uk/genetics/CGP/Census/amplification.shtml

there is only 12 listed, but it might be useful?

HTH

[Danielsbrewer]

In fact our review/database is an extension of the Cancer gene census, see http://amplicon.icr.ac.uk

Answer 4

[Paulo Nuin]

Apart from Nathan's suggestions, I would also try Oncomine and even NCBI's GEO

Answer 5

[D. Puthier]

We have developped TBrowser. It share some features with oncomine (e.g; systematic annotation of expression signature) but it is free. You can search through expression or CGH data for gene clusters highly enriched in any chromosomal region (you will find numerous hits for 1q21 for instance...).