Journal Entry: G:Profiler - bcb420-2022/Emiliya_Stolyarova GitHub Wiki

Started: March 5, 2022. Completed: March 5, 2022.

Objective: Learn how to use G:Profiler (Raudvere et al., 2019) to analyze a list of genes.

Top Terms

The top terms returned in each data source are "immune system process" in Go biologoical process, "Immune System" in Reactome, and "TYROBP causal network in microglia" in Wiki pathways.

How many genes are in the returned genesets?

There are 21029 total genes in Go biologoical process, 10760 in Reactome, and 7806 in Wiki pathways.

How many genes from our query are in the genesets?

There are 424 genes returned in Go biologoical process, 331 genes returned in Reactome, and 286 genes returned in Wiki pathways.

Limit the size of the returned genesets to between 5 and 200 genes in size.

Changing the term size to a smaller size has resulted in a different top term in the Go biologoical proces and Reactome genesets. The top term is now "antigen processing and presentation" in Go biologoical process and "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell" in Reactome.

Ovarian cancer expression subtype

I believe that out of the ovarian cancer expression subtypes, these genes represent the Immunoreactive subtype (Cancer Genome Atlas Research Network, 2011). I believe this since the top terms listed are associated with the immune system.

TFEC gene

TFEC is indicated to be present in the terms titled "response to stimulus", "response to stress", "cellular response to stimulus", and "positive regulation of biological process" in the Go biologoical process geneset.

References

Cancer Genome Atlas Research Network (2011). Integrated genomic analyses of ovarian carcinoma. Nature, 474(7353), 609–615. https://doi.org/10.1038/nature10166

Raudvere, U., Kolberg, L., Kuzmin, I., Arak, T., Adler, P., Peterson, H., & Vilo, J. (2019). g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update). Nucleic acids research, 47(W1), W191–W198. https://doi-org.myaccess.library.utoronto.ca/10.1093/nar/gkz369