Hi folks. After performing differential expression analyses on my single cell RNA sequencing data from ILC2s of mouse origin, treated under three conditions, I generated a list of differentially genes. I afterwards used the Gene Ontology platform to generate a shorter list of genes proven to be present on the surface of mouse cells. Is there a computational possibilty to predict interaction partners of these ILC2 surface genes present on the surface of mouse fibroblast cells?
Thank you in advance for your help.
Hi Anchang,
Computational predictors do exist, however their accuracy is rather low. For your purpose, I would suggest querying databases of known physical interactors from high-throughput experiments such as yeast2hybrid. Check out the Biogrid and IntAct databases.
@Jan Zaucha: Thank you very much for your helpful response. However is there a possibility of ascertaining if these interactions are intercellular or if the interactions are on the surface of the same cell? I am more interested in intercellular interactions.
As you mentioned, you can use gene ontology to identify the proteins present on the cell's surface. Now you want to identify the intercellular interactions. This is more difficult since some of your interactions can occur between proteins residing on the surface of the same cell. To make sure that this is not the case you would have to see which proteins are not present on the type of cell you are looking at - these are the proteins that are down-regulated in your cell type of interest. However, you might filter out too many interactions this way. Alternatively, you can again use the gene ontology annotations to see which proteins are known to mediate intercellular communication: http://www.informatics.jax.org/vocab/gene_ontology/GO:0007154
Finally, another aspect you can look into is where the interaction takes place. You can use 'Interactome Insider' to check which are the interacting residues between each pair of your proteins. Then, you can use the UniProt annotation or Phobius predictions to see where this part of the protein sits with regard to the cell - in the transmembrane region, cytoplasm, or extracellular space. The interactions mediated by the residues residing in the extracellular space of both proteins are most likely the interactions you are interested in.
http://interactomeinsider.yulab.org/
http://phobius.sbc.su.se/