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5 Homework Assignment: g:Profiler
Top term: immune system process (GO:0002376)
Number of genes in geneset: 2683
Number of genes in both query and geneset: 287
Top term: Immune System (REAC:R-HSA-168256)
Number of genes in geneset: 2041
Number of genes in both query and geneset: 217
Top term: TYROBP causal network in microglia (WP:WP3945)
Number of genes in geneset: 60
Number of genes in both query and geneset: 27
The g:Profiler settings were set to limit genesets to those between 5 and 200 genes in size. The top term for GO biological process and Reactome changed, while the top term for WikiPathways is the same.
Top term: antigen processing and presentation (GO:0019882)
Number of genes in geneset: 108
Number of genes in both query and geneset: 40
Top term: Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell (REAC:R-HSA-198933)
Number of genes in geneset: 181
Number of genes in both query and geneset: 46
Top term: TYROBP causal network in microglia (WP:WP3945)
Number of genes in geneset: 60
Number of genes in both query and geneset: 27
Since the top terms are mostly related to the immune system, this list likely represents the immunoreactive ovarian cancer expression subtype.
The TFEC gene is returned in the following GO biological process terms:
- response to stimulus (GO:0050896)
- response to stress (GO:0006950)
- cellular response to stimulus (GO:0051716)
- positive regulation of biological process (GO:0048518)
The TFEC gene is not returned in any Reactome or WikiPathways terms.
Uku Raudvere, Liis Kolberg, Ivan Kuzmin, Tambet Arak, Priit Adler, Hedi Peterson, Jaak Vilo: g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) Nucleic Acids Research 2019; doi:10.1093/nar/gkz369 [PDF].