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Histocat - Differential cell neighborhood analysis

Posted: Tue Apr 23, 2019 11:36 pm
by sbooth
Hi all, hope you are well!

We have 70 samples analyzed by IMC, and they are graded 1-4 in disease severity. Is there a way to see if cell types interact differently between the severity stages?

For example, should we tsne+phenograph on all the samples together, and then run the neighborhood analysis on the different severity groups separately? So we would have 4 neighborhood analyses, then compare the significant interactions among them somehow.

Our hypothesis is that inflammatory cells may interact with structural cells more as the disease severity increases, leading to tissue destruction.

Any thoughts on this would be much appreciated!

Re: Histocat - Differential cell neighborhood analysis

Posted: Wed Apr 24, 2019 2:57 am
by DenisSchapiro
Hi Steve,

I would run tSNE + PhenoGraph on all samples and run neighborhood analysis (1) on 4 different disease states for comparison and on all disease states together. When you run all together, do you see hierarchical clusters enriched in certain cell-cell interactions? When you run them individual, you can compare the heat maps. We have done something similar in the original histoCAT paper.



Re: Histocat - Differential cell neighborhood analysis

Posted: Tue Jul 23, 2019 1:11 am
by sbooth
Thanks Dennis,

Since the neighborhood analysis is run sample-wise. If it is run on a group of 10 samples then separately on another group of 10 samples, shouldn't the results be the same as running on all 20 samples together? The dendogram will look different obviously, but the actual interaction/avoidance values in the matlab data matrices should be the same for the individual samples in both scenarios shouldn't they?

Hope my question makes sense...