How I can study cross-talk from two different tissue using gene expression profile

Question

[adR]

Hi every one,

I am wondering if anyone knows how to find cross-tissue communication signaling using gene expression data set. I have a gene expression profile of two different but inter-connected tissue. I want to get an idea of how these tissues are communicating at the molecular level.

So far, I have done differential expression analysis and enrichment analysis for both tissues using R. I found pathways commonly and differently regulated by both tissues. I have a hypothesis I would like to prove, but I don't know how to approach /study the communications between two tissue using transcriptomics?

I am kind of new to bioinformatics, sorry if I am damping a silly question here. Please also suggest to me what algorism in R helps me?

Thank you so much!

Best
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Answer 1

[Hamid Ghaedi]

To me,  your question (hypothesis) is not valid with regards to biology/genetics. Cells in different tissue for sure have different expression profiles and because of that, you have "two" different tissues!. Indeed what makea a given "tissue identity" is a process (or chain of processes) having gene expression in the core.

However, you can make comparisons between tissue expression profiles to find which signaling pathways are active/deactivate in a certain tissue. Still, it would be really difficult to make a robust conclusion, because you are investigating RNA and not protein level.

[adR]

Thanks for the answer Hamid! One more time If I can ask, is there any tool you know that integrate gene expression data to protein so that I may play and test my hypothesis. If It is totally impossible to test such question using RNAseq data, then I may look for something else. Thanks again!

[Shalu Jhanwar]

To map protein information of the gene, you may want to have a look at UniProt. For the DEGs in different tissues, the functional information at the protein level can be obtained from this resource.