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Comment by yubblegum | Hacker News Reader

> HAR1A is active in the developing human brain between the 7th and 18th gestational weeks.

Anyone know of a resource that layouts the temporal activation patterns for all the genes for the life cycle of a human being?

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Let's assume that you mean activation patterns at the level of single cells. Aside from the ethical issues which make it virtually impossible to obtain the full set of data, there is also the fact that the exact timing of expression is one of the major ways in which development produces variability in phenotype and so can vary wildly between individuals. The closest we have right now might be HUBMAP [0] or HCA [1], but I don't think that those had as objectives covering multiple developmental timepoints.

0. https://portal.hubmapconsortium.org/ 1. https://data.humancellatlas.org/

Thanks!

My group published a cell atlas of the developing human brain in 2023, giving gene expression in single cells from postconception week 5 to 13. It’s on github: https://github.com/linnarsson-lab/developing-human-brain

The NIH BRAIN initiative is working on the next generation of that, covering more timepoints and better spatial data.

Very cool work!

There are various types of triggers for gene activation, some genes turn on/off all the time (housekeeping), some follow the circadian rythm, some are immediate response, some are specific to specific phases of cell division, some are persistently on all the time, etc ,etc. Not sure what type of chart you're looking for.

Thanks. Those modal categories of activations are a great start for organizing a visualization. I wonder what sort of patterns would show up. For example, what role does placement in a specific chromosome have (if at all!) in determining whether the gene is periodic, reactive, systemic, or developmental , etc.

> Not sure what type of chart you're looking for. Just geek curiosity.

> some follow the circadian rythm

Oh no…

As someone who has an highly irregular sleeping pattern, do you know of any or where I can find more info on this?

This can't be done reliably but you may want to look at Tabula Sapiens which doe some of what you'd like. It's not an obvious problem in lots of ways.

Thanks. Suprised no one has made a visualization (even if it has gaps).

> It's not an obvious problem in lots of ways.

Care to expand on this?

Link for others:

https://www.science.org/doi/10.1126/science.abl4896

https://maayanlab.cloud/Harmonizome/dataset/Tabula+Sapiens+G...

I think people who aren’t already experts in this aren’t the right ones to try. For experts, the technical questions are very evident.

You may also like GTEX and the Human Protein Atlas (which also has gene expression data)

As others have said, a complete dataset for that is basically impossible. You would have to monitor every cell type in an individual from the moment of conception until death. Maybe in a couple hundred years we’ll have nanotech robots that could do that, and our overall morals and ideas of what constitutes ethical research will have changed enough that we allow the creation of such humans with these robots inside them.

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