Question of the Month #1: ALAS1 and Valproic Acid

[MarkDWilliams]

The use of the Friday standup calls to cover a more nuanced question in greater depth was discussed at the most recent Relay meeting, and this is the first of those questions of the month. Please use this ticket to discuss the question, potential approaches to formulating queries to address it, and any possible blocking issues. We can discuss these points further and touch base on our progress and next steps during the normally scheduled Friday stand up time.

Kick-off challenge question of the month:

Submitting team: SRI

SME: Stephen Ferguson, PhD, Scientist, Molecular Toxicology and Genomics Group within the Biomolecular Screening Branch of the National Toxicology Program at the National Institute of Environmental Health Sciences Background and challenge question: “I have started to connect the dots a bit between genes that are reversibly changed in vitro for liver models versus clinical and mechanistic data. … For example, I saw ALAS1 gene is clearly induced in a highly potent manner by valproic acid, and when taking the chemical away, the signal (along with many other genes) goes away, while others remain. A quick Google search didn’t show a lot of connection between ALAS1 and valproic acid. However, mitochondrial function was linked to ALAS1 and valproic separately. So, I’m wondering what might be the best ways to do this kind of next-level search that would connect chemical-gene targets-mechanisms/pharmacology-pathology across these four data types.”

[karafecho]

Thanks for running the valproic acid and CBD queries, @colleenXu. I sent a summary of results to Paul Watkins and will be sure to keep you informed.

[cbizon]

For posterity here is a link to the enrichment notebook.

[karafecho]

Closing with comment in #233 ...