I am currently analysing some RNA-Seq data from human primary fibroblasts. I noticed in the following paper (https://www.nature.com/articles/ncomms15824) that the expression of hox genes was used as a proxy for biopsy site.
Would anyone have any potential scripts or other resources they could point me to? I'm just not sure how to code it/which hox genes to include.
Many thanks for your time,
Rob.
I think your answer is in the supplementary materials of this paper that you have cited https://static-content.springer.com/esm/art%3A10.1038%2Fncomms15824/MediaObjects/41467_2017_BFncomms15824_MOESM399_ESM.pdf on pages 25-26.
The authors have used the expression of hox genes from all the samples to cluster that data matrix and then used those clusters to create a new factor variable with x levels and used it as an adjustment factor in the regression model.
If you are asking how to create this cluster variable, then one way would be to use the 2 functions in R, you can google for a detailed usage
hclust and then cutree
You can also see a quick example from one of our project code
https://github.com/uhkniazi/BRC_FOG1KO_John_PID_25/blob/2f31428900bcfb76404c86242760da296bb11bf1/04_fastQC_trimmed.R#L192
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