RNA-Sequencing in human primary fibroblasts: How do I control for biopsy site?

Question

[robert.flynn.21]

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.

Answer 1

[jv]

According to the supplementary methods in the paper you cited:

To control for this effect we performed hierarchical clustering of the RNA expression across all samples based only on the HOX genes (identified as genes with names starting with “HOX”) which revealed four major sample clusters

It sounds like they did not assign specific biopsy sites so much as cluster samples based on HOX gene expression in order to define an additional factor (i.e. the HOX expression cluster assignment of the sample) in their DE model design.

There is a Biostars tutorial Unsupervised clustering on gene expression data that may be a good starting point for this.

Answer 2

[robert.flynn.21]

Yeah you're right, they did just cluster the samples based on HOX expression rather than assign a biopsy site per se. I am working through the tutorial you linked now.

It's very helpful thankyou!