Further Reducing Gene Ontology list

Question

[Parichitran]

Dear all,

step1: I did Gene ontology for my 1247 genes with Gprofiler(species=Mice,termsize=1000) through their webpage and got all of the ontologies with Padjustvalues.Coming to BP-G0s its around 275 GOs

Step2: Then I used revigo(tiny,Sematic method:Lin) to remove reduncy terms in those 275 GOs.So in the end i got the following summerised GOs(60 in number).But still in my lists some overlapping processes are not reduced like metabolic,cellcycle etc....Can anyone please suggest how i can reduce these overlapping process into single process.Thanks in advance

intracellular protein transport peptide metabolic process generation of precursor metabolites and energy ribosome biogenesis carboxylic acid metabolic process aerobic respiration mitochondrion organization ncRNA metabolic process mitochondrial gene expression membrane organization protein folding endomembrane system organization mitotic cell cycle process apoptotic signaling pathway proteolysis involved in protein catabolic process carbohydrate derivative biosynthetic process vasculature development regulation of mitotic cell cycle regulation of catabolic process positive regulation of apoptotic process regulation of anatomical structure morphogenesis response to hormone protein hydroxylation response to oxidative stress regulation of protein localization regulation of protein catabolic process regulation of plasma membrane bounded cell projection organization plasma membrane organization extracellular matrix organization external encapsulating structure organization extracellular structure organization carbohydrate metabolic process cell division positive regulation of cell migration sulfur compound metabolic process regulation of anatomical structure size positive regulation of smooth muscle cell proliferation gastrulation process utilizing autophagic mechanism organic hydroxy compound metabolic process regulation of aerobic respiration ameboidal-type cell migration proteasome assembly enzyme-linked receptor protein signaling pathway positive regulation of intracellular signal transduction peptidyl-proline modification epithelial to mesenchymal transition regulation of transcription by RNA polymerase I cellular component disassembly regulation of binding viral process viral release from host cell cellular modified amino acid metabolic process supramolecular fiber organization response to fluid shear stress regulation of amide metabolic process cellular homeostasis smooth muscle cell proliferation tissue migration regulation of cytokine production

[young_bioinformatician]

I would recommend WEGO, but unfortunately, It is not up-to-date.. Last update is 2018.

[Parichitran]

Yeah ,young_bioinformatician it is unupdated.

Answer 1

[geneontologyhelp]

You might be interested in the standard GO tools GO Term Finder and GO Slim Mapper. Each will work on your original list of 1247 mouse genes. I've included links to both the SGD version as well as a version hosted by Princeton- they are the same tool, written by the same people, just hosted/maintained by different groups. The Princeton tool is a little better for mouse, but if other people have a similar question they might find the SGD tool suits their needs.

• GO Term Finder finds significant shared GO terms in your gene list. It may select multiple terms in the same "branch". Upload your full gene list as a file. Princeton GTF OR SGD GTF
• GO Slim Mapper takes all of the terms your gene list and maps them to a preselected set of "bins", and usually has a leftover "unmapped" remainder (you can run this remainder through the tool again to see if you get any more bins). You can use the "Generic GO-Slim: process" or load the mouse-specific slim (aka subset) available on our downloads page, or even curate your own slim using a combination of GTF results and the terms you are most interested in. Again, a list of your size should be uploaded as a file. Princeton GTM OR SGD STM

From your description, to get non-redundant terms, you might find the Slim Mapper the better tool for your purpose.