defining function of list of genes

Question

[zizigolu]

Hi

I have a list of gene symbols like PIL1, .... how I can see which of them is related to cell elongation?

I performed annotation with DAVID, affymetrix, plexdb, Agrigo...but they could not tell me what is want but when I check one by one in google I found some of them related to cell elongation but impossible to check all manually...is there anyway to check this function?

Thank you

[zizigolu]

yes but GO is too generic

[User 59]

Can you please use the add comment function to respond to particular answers Feresheh? I've had to move your comment to the top level as you added it as an answer.

[zizigolu]

sorry, but I could not get you..in this post I did not add any answer, only I left comment

[Ram]

If you are replying to an answer, click on the gray Add Comment button. See:

The interface then shows you a text box to add your comment in:

Once you're done typing, click the green Add Comment button to add the comment. Do not add your comment as a new answer.

[zizigolu]

OK thank you

Answer 1

[andrew.j.skelton73]

Have you tried GO annotation?

Answer 2

[Veera]

Try Biofilter . You can annotate the genes for the groups and sources, which will include the gene function. It may help!

[zizigolu]

Thank you I will try now

Answer 3

[ivivek_ngs]

I believe there are different GO tools that might end up giving different results. First of all one need to understand that manual gene by gene search is not significant enough to term the GO you have been looking for. That is where we use the enrichment term where you try to see how your gene have been enriched across different GO terms with significance , and these tools all vary with their knowledge base on which they are built. So you can always test with more tools like Amigo2, PANTHER, Enrichr and try to play with the best fit filtering strategy for selecting terms. I always go with FDR unless am focusing on something particular. Since you are focusing on a particular term, there might be different GO terms that converse into cell elongation as well. So trying looking into the output carefully. Looking for a single category might not term it to be significantly up the ladder, since you might have genes that have higher significant enrichment for other category. So you take into account all chores.

[zizigolu]

Yes you all right thanks