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I want to do pathway enrichment analysis in python using scipy.stats.hypergeom.sf function to select pathways that are significantly enriched in at least one tissue.

my data:

Enrichment  CANCER_TYPE PATHWAY
11.6    Breast Carcinoma    Cell cycle/DNA replication
2   Breast Carcinoma    Protein stability and degradation/DNA replication
2.8 Breast Carcinoma    EGFR signaling/DNA replication
4   Breast Carcinoma    p53 pathway/DNA replication
0   Breast Carcinoma    PI3K/MTOR signaling/DNA replication
1.2 Pancreatic Carcinoma    Mitosis/RTK signaling
3.3 Pancreatic Carcinoma    EGFR signaling/RTK signaling
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  • $\begingroup$ what is "Enrichment"? usually this kind of data comes in the form of a list of genes with annotations and some sort of background set of annotations for genes in a genome. At a minimum, we would expect some count of genes/gene annotations, which is necessary to get the numbers to plug into a hypergeometric test. Different tools will count annotations differently, perhaps tell us more about where your data table comes from? $\endgroup$ Commented Apr 18, 2022 at 20:41
  • $\begingroup$ Could you please add some more detail to your question? Context helps a lot. It's great that you've included input data, but we don't know how that data is generated, or what the 'Enrichment' field means. $\endgroup$
    – gringer
    Commented Apr 19, 2022 at 3:21

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