enrichment tool(s)

[ValWood]

We should look into bringing enrichment into PomBase

Options: https://metacpan.org/release/GO-TermFinder

hierarchal filter, best per parent https://biit.cs.ut.ee/gprofiler_archive2/r1760_e93_eg40/web/ @ValWood contact to see if web code available and ask why the hierarchical filter removed. Test the output compare GO term finder (taking difference in datasets into account)

InterPro

[ValWood]

I have been mening to go through raymond Lee's slides showing SOBA, ona call.

Basically a way to display ontology data in a simplified graph:

compare

to

this tool could be useful to visualise enrichment results (or on gene pages)

[ValWood]

RGD have also developed a generic enrichment tool. Will add a link when published.

[kimrutherford]

Will add a link when published.

https://academic.oup.com/genetics/article/220/4/iyac005/6516514

[ValWood]

or https://www.biorxiv.org/content/10.1101/2023.02.20.529262v1

[kimrutherford]

Edit 2024-08-28 kmr: this API is unlikely to be supported so it might not be what we need.

---

I couldn't find the code for the Panther enrichment tool but it's possible to do enrichment via the API: https://www.pantherdb.org/services/openAPISpec.jsp

API requests return quite quickly so that might be a way to get an enrichment integrated into pombase.org without re-inventing the wheel.

They have two APIs "Enrichment (Overrepresentation)" and "Statistical Enrichment". I don't understand the difference.

There aren't many options and probably the problem you mentioned about regulates is still an issue.

Below is an example of the JSON returned.

[
      {
        "number_in_list": 8,
        "fold_enrichment": 0.1127690842740848,
        "fdr": 6.20395058473066e-25,
        "expected": 70.94142912924639,
        "number_in_reference": 1873,
        "pValue": 7.321159528830139e-28,
        "term": {
          "id": "GO:0009058",
          "label": "biosynthetic process"
        },
        "plus_minus": "-"
      },
      {
        "number_in_list": 3,
        "fold_enrichment": 0.054028775966582746,
        "fdr": 7.278220055543924e-22,
        "expected": 55.525966419367435,
        "number_in_reference": 1466,
        "pValue": 1.0306660451560901e-24,
        "term": {
          "id": "GO:1901564",
          "label": "organonitrogen compound metabolic process"
        },
        "plus_minus": "-"
      },
      {
        "number_in_list": 17,
        "fold_enrichment": 0.2123155399935628,
        "fdr": 6.376165142050856e-22,
        "expected": 80.06950409996095,
        "number_in_reference": 2114,
        "pValue": 1.053414113626528e-24,
        "term": {
          "id": "GO:0043170",
          "label": "macromolecule metabolic process"
        },
        "plus_minus": "-"
      }
]