finding co-expression genes

Question

[seta]

Hi all,

I have several gene list of plant and animal species that each list contain about 1000 genes, I'm trying to identify co-expressed genes for each list. I knew some tools, like ATTED-II (for plant), but as I found there, this tool dose not support a gene list with more than 10 query genes. Is there any suggestion and introduction a tool, which be able to handle a very large genes list to recognize co-expressed genes for that gene list. Thanks a lot for your time and help in advance.

[smilefreak]

Would it be reasonable for your to download coexpressed files and perform generate your predictions that way?

http://atted.jp/download.shtml

Then for each of the genes, it seems like they get their own file, you could get the relevant file. Then by using the mutual ranks score they provide in the files you should be able to extract the most significantly co-expressed genes.

I do not know of a tool to do exactly this, but I think with a googlefu and depending on your experience, maybe a few more questions on biostars would get you through the process.

Answer 1

[seta]

Thanks for your reply, but I want to have those genes that co-expressed with just my gene list not all genes.

[smilefreak]

I think from the website each gene gets it own file, so you would be able to just select those 1000 files and then pick the highest ranking co-expression values. I think at least.

[seta]

Thanks a lot for your reply, could you please let me know how to extract those genes (from the downloaded co-expressed file) that co express with my selected gene list?