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Consider a different gene set example on the front page #2451

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cmungall opened this issue Mar 7, 2025 · 0 comments
Open

Consider a different gene set example on the front page #2451

cmungall opened this issue Mar 7, 2025 · 0 comments

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@cmungall
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cmungall commented Mar 7, 2025

The front page has four gene sets to cycle through, these are "hallmark" gene sets from msigdb, so while semi-artificial they should provide relatively good signal.

The first option is for the msigb Notch hallmark set. We'd expect this to give a clear signal for the Notch pathway, but the results on the main GO site seem a weird hodge podge of developmental processes with no cohesive story (cerebellar molecular layer formation / hemocyte differentiation / angiogenesis).

IBA restricted (via functionome) gives a much simpler story (Notch + Wnt signaling).

Here is a perplexity deepresearch report on the same gene set: https://www.perplexity.ai/search/what-is-the-likely-underlying-t7GiIzw7SraQCX_GT9gLEQ

We should pick gene sets that show GO in the best light (or restrict human to IBA by default)

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