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