Hey, I want to perform a GO term enrichment analysis by comparing a list of affected protein to all protein identified and/or genome.
First I performed GO Slim mapper at SGD and then performed Fisher exact test on each GO term individually. After doing all of that I realized I should probably have compared affected proteins to all proteins identified and not the the entire genome.
I have noticed that a lot of papers use DAVID so I uploaded a gene list and the background list but my analysis kinda stops up. I get that there are different levels for GO Annotation, but I just do not know how to use them.
I want to know - does the affected proteins have a specific subcellular localization? - does the affected proteins share biological function? - does the affected protein interact with specific protein complexes?
Any help is highly appreciated!
Also, most papers presents their data with a bar graph that looks like it has been generated by the same source. Does anyone know how to do this?