Co-expression analysis for genes coexpressed with gene X, genes X and Y, etc.

Question

[jparker4]

Hi, I have been asked to perform a co-expression analysis to look for genes that are co-expressed with several genes of interest. The individual has requested that I look for genes co-expressed with each of the genes of interest, then look for genes that are co-expressed with two of the genes of interest (repeated in all possible different combinations) and then with three genes of interest. Is this possible? And if so, what would be the best package/method for performing such an analysis.

Thanks

Answer 1

[Martombo]

I guess you could start by checking which (if any) of your genes of interest are significantly coexpressed. In that way you could use pairs / groups of genes to define a profile of expression. After that, you can determine which other genes are most coexpressed with these modules, or each of your genes of interest.