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G Profiler

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Ben Tudor Price edited this page Apr 6, 2023 · 4 revisions

Time Estimate

  • Estimated Time Required: 30 mins
  • Actual Time Required: 30 mins

Notes

  • Selected setting "Choose Ensembl ID with most go annotations" for ambiguous genes.

Questions

  1. What is the top term returned in each data source?
  • GOBP: immune system process
  • REAC: immune system
  • WP: Allograft rejection

  1. How many genes are in each of the above genesets returned? (hint, in the Detailed results tab of g:profiler results if you click on the arrows next to the stats heading you will be able to see the number of genes in a term, number of genes in your query and number of genes in your query that are also in your term)

  2. How many genes from our query are found in the above genesets?

  • format: T-Q-T&Q
  • GOBP: 2683-430-290
  • REAC: 2041-334-220
  • WP: 88-291-32
  1. Change g:profiler settings so that you limit the size of the returned genesets. Make sure the returned genesets are between 5 and 200 genes in size. Did that change the results?

T-Q-T&Q

  • GOBP: 108-430-42
  • REAC: 181-334-47
  • WP: 88-291-32

Yes, we have

  • GOBP: antigen processing and presentation
  • REAC: Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
  • WP: Allograft rejection
  1. Which of the 4 ovarian cancer expression subtypes do you think this list represents?

Of the four gene expression subtypes: mesenchymal, immunoreactive, proliferative, and differentiated, iven the strong involvenemnt with immune processes, I'd say it's most likely to be immunoreactive (Koshiyama et al., 2017).

Bonus: The top gene returned for this comparison is TFEC (ensembl gene id:ENSG00000105967). Is it found annotated in any of the pathways returned by g:profiler for our query? What terms is it associated with it g:profiler?

TFEC GOBP:

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 3 5 involved_in negative regulation of transcription by RNA polymerase II IDA 9256061
GO:0006355 5 regulation of DNA-templated transcription IEA  
GO:0006357 3 5 involved_in regulation of transcription by RNA polymerase II IBA 21873635
GO:0034605 3 5 involved_in cellular response to heat IEA  
GO:0045944 3 5 involved_in positive regulation of transcription by RNA polymerase II IDA 9256061

No enrichment for above terms in our dataset. No annotations in WP or Reactome.

References:

Koshiyama, M., Matsumura, N., & Konishi, I. (2017). Subtypes of Ovarian Cancer and Ovarian Cancer Screening. Diagnostics, 7(1), 12. https://doi.org/10.3390/diagnostics7010012

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