I have a set of differentially expressed genes with their Uniprot IDs. The dataset is from a tomato and consists of differential expression over time. I want to make a chart to represent changes in gene ontology enrichment over time. However I cannot find good (preferably web based) programs with gene ontology enrichment for my tomato species. I've tried DAVID, it hasn't been updated for the last 5 years. I tried AgriGO, but for some reason it doesn't recognize my Uniprot gene IDs. I've had moderate success with PANTHER, but the program only gives out very broad GO terms (like "metabolic process") to the data. Is there another good alternative program that I can plug in p-values and Uniprot ids like this:
K4ARR1
Q40128
K4D6C6
and get enrichment outputs that I can manipulate? Thank you for the help.
I have, the program has no background reference for Solanum Lycopersecum, It will take the uniprot IDs, run them through the few available species, and then report no results.
I think bingo accepts uniprot ids even though I could not work with BINGO plugin in cytoscape, but you try that. Also try GOrilla and GOTERMFINDER which I have not tried myself yet.
GOrilla doesn't have the tomato species and doesn't recognize the GO IDs that I pair with my gene IDs while trying to make a new database. I'll try cytoscape with BINGO and come back with results.
I would suggest you babelomics but for me it is working very slowly. Maybe if you register and try a real example it will work faster. If you have some R programming skills, I would suggest you to try with it.
Okay, so here's how I ended up "solving" this issue. I went back to my list of all my genes in my transcriptome. I converted the sol IDs to Uniprot IDs and then used the Uniprot website to get the GO IDs for each of my genes. I then went to the website AgriGO. AgriGO has the option of using your own custom background dataset to compare your inputs with. So, using my transriptome data as a background, I got all of the differentially expressed genes that met my cutoffs and ran my gene enrichment analysis against my transcriptome. This way I could use and IDs I wanted as long as I had the proper GO terms right next to them. Although AgriGO was built with agricultural research in mind, this function means you can basically replicate these steps with any organism as long as you have the right GO terms for the genes in your transcriptome. I'm pretty happy with the results now.
I know that Bingo gives you the option to do this, but as of three days ago the cytoscape website was down so I couldn't get cytoscape to get the BINGO plug-in. I also really need to learn R, seeing that many analysis programs use this language and right now it looks like the standard. Thanks for the help!
Thank you for your complete explanation, yes you definitely right about R, me also got with R even I can do all of a demanding workflow for maximum of ideas...hope a day I could learn this language...
Have you tried this one?
http://geneontology.org/
I have, the program has no background reference for Solanum Lycopersecum, It will take the uniprot IDs, run them through the few available species, and then report no results.
I think bingo accepts uniprot ids even though I could not work with BINGO plugin in cytoscape, but you try that. Also try GOrilla and GOTERMFINDER which I have not tried myself yet.
GOrilla doesn't have the tomato species and doesn't recognize the GO IDs that I pair with my gene IDs while trying to make a new database. I'll try cytoscape with BINGO and come back with results.
Good job, please let me know about your BINGO result
I would suggest you babelomics but for me it is working very slowly. Maybe if you register and try a real example it will work faster. If you have some R programming skills, I would suggest you to try with it.