Question regarding pathways and cell types

Question

[Nemo]

Hi everybody,

I have a question regarding the cell types and pathways. First, I would like to get some information about the similarities and differences between pathways in different cell types. Do pathways have the same definition (the involved genes and their relations within each pathway) in all cell types?

and second, if the answer is yes (there are differences), is there any database for such information?

Answer 1

[Matthias Zepper]

By and large, pathways and signalling cascades are conserved. Therefore, you will find many similarities within a particular pathway - not only between cells, but also between organisms - that is why for example much of the foundation of developmental biology could be unravelled based on Drosophila and Xenopus model organisms.

Yet, there are also distinct differences, between organisms (-> orthologs and paralogs) as well as within cell types of one organism and even dependent on the context. Take any of the well known pathways, and you can find ample of reviews detailing the subtleties say...in cancer. Wnt-signalling or JAK-STAT are examples. In addition, pathways are of course interconnected: The Ral pathway can e.g. be activated in a Ras-dependent or Ras-independent manner (canonical Ras singalling happens via MAPK).

There have been works simulating signal responses and gene-regulatory networks in silico, but unfortunately I do not know respective databases.

Answer 2

[LauferVA]

This is a huge issue. The answer here is to re-construct pathways and signaling cascades based on single-cell RNA seq data, one cell type at a time. If someone took the right approach here (and had the requisite data), would certainly be a high impact manuscript.