Midjourney image

For this week's post, I thought I’d mess around a bit with the CellXGene tool provided by the Chan Zuckerberg Institute.

It's based on a big dataset of individual cells, classified by tissue, cell type, and disease state, and their gene expression profiles (single-cell RNA counts).

You can automatically compare how gene expression looks different between sick and healthy individuals, for a variety of diseases, and drill down into which cells/tissues are different and how.

It's a fascinating toy and a great way to generate hypotheses.

Here, I’ll do it for Alzheimer's, comparing 138,438 Alzheimer's brain cells to 9,203,998 normal/healthy brain cells to see what the most “differentially expressed” genes are, and what that might tell us about how the disease works.

Top Hits

LINC01609

1.6x overexpressed in Alzheimer's, d =4.203

This is a non-protein coding RNA. Typically most expressed in the testis. In [...]

---

Outline:

(01:13) Top Hits

(01:16) LINC01609

(01:21) 1.6x overexpressed in Alzheimer's, d =4.203

(01:50) SLC26A3

(01:55) 10.6x overexpressed in Alzheimer's, d = 3.310

(04:06) RASGEF1B

“Fun With CellxGene ” by sarahconstantin

LessWrong (30+ Karma)