How can I cluster the gene expression in the tissue between different species?

Question

[cherhorowitz]

In the transcriptome comparison, rat brain tissue is more similar to mouse brain than rat heart (Figure 1). Now, I have the gene expression of each tissue in two species (Figure 2), how can I cluster these two data? Ultimately I want to look like Figure 1.

1. Maybe I need to find out the orthologous gene first?
2. I think I can use "dist" and "hclust" in r, but now one of the gene lists is for rat and the other is for mouse.
3. And I have already normalized the gene expression.

Thank you so much.

Answer 1

[Ming Tommy Tang]

Hi, Yes, you need to find the gene mapping between species if you want to plot them together. Be aware of the batch effect; tissues should be clustered together. see https://f1000research.com/articles/4-121/v1

All are covered in my book https://divingintogeneticsandgenomics.ck.page/products/cell-line-to-command-line

Answer 2

[Michael]

You can find the gene-to-gene mappings in ensembl biomart. Best to use only one-to-one single-copy orthologues.