Analysis of list "interesting" proteins from protein array

Question

[moranr]

Hi,

Using a protein array I have X number of proteins that are created based on an immune response to a cancer in a species. What sort of analysis could I do , computationally, with this data. I would like to understand what is so special about this X number of proteins if possible.

My ideas so far :

• Look at a sequence level, how closely related are the "interesting" proteins with relation to a random sampling of other proteins on the array.

• Look at GO enrichment for the "interesting" proteins.

Anything else that I could potentially look into ?

Thanks

Answer 1

[Jean-Karim Heriche]

You could do comparison/enrichment analysis for all kinds of features you can think of. GO annotations and sequence annotations (e.g. domains) are just two types of features. You could also look at expression in tissues/developmental stages, phenotypes, protein interactions... You can also expand the information content by transferring features from orthologs. Besides enrichment analysis, you can also look at similarity measures between genes derived from the features (e.g. a la GeneMANIA).