How to view the list of over or under expressed genes in any particular cancer?

Question

[ujwalda]

Hi, I am curious to know how we can see a list of highly or lowly expressed genes in any specific cancer relative to its normal tissue, let's say for e.g., melanoma? I have found that cbioportal gives frequency of alteration/mutation for the genes associated with any cancer. But I want to know the expression level change of genes. Thank you

Answer 1

[ivivek_ngs]

You can use the GDAC Firehose browser and check for the data they have analyzed. But you can only view them with one gene at a time. Check the link. Remember these are TCGA data only, for certain cancers you might not even have the normals as in the case of Ovarian Cancer. Most of them have usually frequency of alterations in patients. If you want to retrieve the expression estimates for particular cancer then the best will be to download the FPKM or RPKM data for that cancer and then plot for yourself by using your own list of genes.