Shoutout to Brett Phinney for tipping me off to this super cool tool!
Gene Ontology enrichment is a hot topic these days! Problem is, I don't have the time to learn an R script to do this stuff.
The GOrilla is a web-based solution! It is 1) Fun to say (say it with me -- "GooooooooRILLA!!!) 2) Its real easy and fast and 3) It might be a rapid and free way to make some sense of that big list of differentially regulated genes/proteins you're looking at.
First of all, you need your background protein list. So...everything you identified.
If you're using PD 2.1 you can just start at your protein list and Export that top layer to Excel (click to expand)
Next you need to filter your list down to your differentially regulated list. (Thank you Dr. Horn for your assistance with this filter. It was driving me nuts.)
This filtered all of my data down to the ones that are up- and down-regulated beyond an
Repeat the Export. In my case I end up with 148 differentially regulated proteins.
Now, go into both of the Excel spreadsheets and select the column that has your Universal Gene Identifier. Wait. You don't have one?? Reprocess your consensus with the Annotation node. That should do it. Maybe do that before you do all the steps above. It'll look like this.
Now, this is SWEET! Just highlight the whole column (first the differential and then your background list) and set up the GOrilla to take both.
Tell it what organism it is looking at copy in the lists (it is VERY forgiving of formatting!) and hit the Search button.
And it's gonna kick out an awesome pathway like this thing!!
GooooooooooooRILLLA!!!!!
Sorry it doesn't fit on the screen, I only had 20 minutes between meetings!! This is cool enough to frantically put together, right?
It is quite similar to a lot of other GO tools, including the same issue: They all miss the info(date/version) about the used database. That is the case with all GO tools like LAGO, DAVID.
ReplyDeleteI would suggest looking into cluoGO as well. It is a plugin for cytoscape that fully allows you to adjust all of the settings, including updating to the most recent database version of uniprot.
I would really like to try this! But I do not see an option for abundance ratio under my filter options..... I must be doing something incorrectly? I am using PD 2.1...... ???
ReplyDeleteI would love to try this! But I do not see abundance ratios as an option in my filter list. I must be doing something incorrectly..... I am using PD 2.1???
ReplyDelete