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I have a list of genes (n = 120) that are involved in breast cancer. And I have a list of differentially expressed genes (n = 70) that are present in the breast cancer gene list. My question is: Are differentially expressed genes significantly more likely to be breast cancer related vs non-differentially expressed genes? which statistical test will be suitable to address this question and how I can visualize its results in R.

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  • $\begingroup$ I would suggest using an existing tool to evaluate this issue, such as the GO enrichment analysis toolkit: geneontology.org/docs/go-enrichment-analysis. Some of the details are finicky, there are a lot of people who have thought very hard about the issue of annotating genes and GO is what people have settled on, rather than a bespoke list of BC genes. If you must visualize this (rather than simply report the numbers or have a table of enriched categories, which I'd prefer), I'd use a Venn diagram, which you can google for R. $\endgroup$ Jun 14 at 15:47

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