I am new to Gene Ontology. I have a couple of lists of common DEG's from a couple of diseases.
I want to shortlist the number of genes to get candidate genes using gene ontology.
I am looking for using David tool or shiny go tool for analysis. Can someone help me out in understanding how to get enriched terms (how to interpret the charts and results obtained from gene ontology tools).
Google is your friend when looking for tutorials. Here is a reasonable looking tutorial.
Regarding interpretation, have a look at how papers report GO results, or find other tutorials of which there are dozens easily found online. Generally speaking, GO results offer only a broad picture of what is going on, so you'll have to fill in the blanks with a solid understanding of the outlier genes you have, what is published about them, etc..
In terms of using tools, this is species dependent. Model organisms are easier, as many bioconductor packages exist for annotations to use tools like topGO. As well as almost any of the web services. If you are working in a non model, you can either use 1-to-1 orthologs of a well annotated species, or try to annotate GO terms in the transcriptome yourself and then use something like gProfiler2.
Thank you for your help! I am not too comfortable using R packages for my analysis. I prefer using online tools as I am not so familiar with coding. The species is Homo sapiens, datasets and deg's for which I found from GEO2R. After making Venn Diagram for common genes between different diseases, I got a list of genes for each pair of diseases. I want to know the significantly enriched genes in order to shortlist the gene set I have obtained. Can you please suggest comprehensive online tools for this. Through my research and watching tutorials I have come to understand that for each gene ontology term, there are a number of genes associated with it (from the gene list I have submitted in the query) and I will have to manually find which genes were enriched significantly by clicking on each go term hyperlink. I hope I am correct in understanding how i am supposed to do the interpretation. I appreciate your time and efforts, thank you!
Please do not add answers unless you're answering the top level question. Instead, use Add Comment or Add Reply as appropriate. I've moved your post to the right location this time, please be more careful in the future.
If you use the above link, and let us know any specific questions, we can help. That help page is intended to accompany the widget on our homepage: https://geneontology.org, which can be used with no coding experience. PANTHERdb, which powers our EA tool, has more advanced tools than our quick-fire widget including the ability to load background lists ("reference list"), etc. PANTHER has a quite extensive help doc, or we recommend reading our Gene Ontology Handbook- this is free, if you have any problems accessing it please contact us for the full PDF. See also the PANTHER tips page.
Thank you for your help! I am not too comfortable using R packages for my analysis. I prefer using online tools as I am not so familiar with coding. The species is Homo sapiens, datasets and deg's for which I found from GEO2R. After making Venn Diagram for common genes between different diseases, I got a list of genes for each pair of diseases. I want to know the significantly enriched genes in order to shortlist the gene set I have obtained. Can you please suggest comprehensive online tools for this. Through my research and watching tutorials I have come to understand that for each gene ontology term, there are a number of genes associated with it (from the gene list I have submitted in the query) and I will have to manually find which genes were enriched significantly by clicking on each go term hyperlink. I hope I am correct in understanding how i am supposed to do the interpretation. I appreciate your time and efforts, thank you!
Please do not add answers unless you're answering the top level question. Instead, use
Add CommentorAdd Replyas appropriate. I've moved your post to the right location this time, please be more careful in the future.If you use the above link, and let us know any specific questions, we can help. That help page is intended to accompany the widget on our homepage: https://geneontology.org, which can be used with no coding experience. PANTHERdb, which powers our EA tool, has more advanced tools than our quick-fire widget including the ability to load background lists ("reference list"), etc. PANTHER has a quite extensive help doc, or we recommend reading our Gene Ontology Handbook- this is free, if you have any problems accessing it please contact us for the full PDF. See also the PANTHER tips page.