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 [...]
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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
(04:10) 5.5x overexpressed in Alzheimer's, d=3.267
(05:17) LINGO1
(05:20) 3.9x overexpressed in Alzheimer's, d=2.799
(06:11) INO80D
(06:15) 2x overexpressed in Alzheimer's, d =2.244
(07:21) What's Going On Here?
(09:55) What Does CellxGene Get You?
The original text contained 2 images which were described by AI.
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