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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!
Best,
Steve

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.

Best

Denis

Re: Histocat - Differential cell neighborhood analysis

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

I see in the saved neighborhood matlab data file there are a few matrices of interaction data. Am I correct that I would want to use "Matrix_Delta_cut_noNaN" to reproduce the clustergram?

Also, how do you retrieve the specific number of interactions between two cell clusters. i.e. for each sample how many interactions between cell phenotypes 1_2??

Thanks again,
Steve

Re: Histocat - Differential cell neighborhood analysis

Posted: Wed Jul 31, 2019 7:38 pm
by DenisSchapiro
Dear Steve,

This is a pretty unique and tailored question. I will respond via email with your data example.

For the Clustergram, use the command: view(Delta)

Best

Denis