Obtain gene ontologies using curated GO list as database
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2.7 years ago
yepeh72919 ▴ 10

Hello all, I have conducted ChIP-seq and gene ontology using Rosalind, which uses Homer to find the peaks and GO: biological processes. Image

My goal is to obtain cardiovascular epithelial ontologies so I can identify some gene of interest.

It seems like all my ontologies are related to the nervous system/neurons, whereas I am more interested in cardiovascular epithelial ontologies. I think that this is because the genes in the gene list overlap between these different systems. What can I do to obtain the ontologies that I want?

Some things that I have tried:

  • Used KEGG database (through enrichR) instead of GO, still obtained ontologies that are unrelated to what I am interested in.

  • Someone in a previous post informed me that AgriGO may be helpful but the server is down right now.

  • I am also considering the following: Instead of using GO: biological processes, I can use a curation of genes (found on QuickGO) as my database, instead of GO: biological processes or KEGG. https://www.ebi.ac.uk/QuickGO/targetset/BHF-UCL

    • Is this feasible, or will this be cherry picking my data? If this is ok, can anyone please point me in the right direction in order to do this?

    • I do not have any experience with R but I am willing to learn to obtain appropriate gene ontologies, so I can find a gene of interest. I have read other posts that mention clusterProfiler, but it was hard to understand the documentation to find if I can even use a customised database.

Once again, thank you all for your time.

gene ontology ontology go ChIP-Seq R • 859 views

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