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data2intelligence / SpaCET

Spatial Cellular Estimator for Tumors
GNU General Public License v3.0
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Clarify Malignant Cell State A and B #34

Open rln0005 opened 2 weeks ago

rln0005 commented 2 weeks ago

Hi SpaCET team,

Quick question regarding the Malignant Cell State A and Malignant Cell State B. Can you clarify what the differences are between these, and how they are calculated? Are they comparable across samples? (ie, malignant state A is the same for sample 1 and sample 2, or do they differ based on sample-specific factors?) I assumed they were based on shared copy number profiles for the sample, but not necessarily comparable across samples. Just wanted to double check.

Thanks in advance!

beibeiru commented 2 weeks ago

Hi, Rebecca,

Malignant Cell States are identified from the clustering results of inferred malignant cell regions based on their expression profiles rather than copy number profiles. Thus, different Malignant Cell States have various function phenotypes. They are not comparable across samples because each ST sample was analyzed independently.

In order to annotate the identified Malignant Cell States, you can follow this tutorial to calculate the known cancer cell state score, and then compare them. https://data2intelligence.github.io/SpaCET/articles/GeneSetScore.html#calculate-cancer-cell-state-score

Best, Beibei