Biostar Beta. Not for public use.
Is there a data base, tool or method I can use to find out which of my genes code for cytokine receptors?
0
Entering edit mode
14 months ago

I have a list of over 600 differentially expressed genes from my single cell RNA seq data analyses. I want to proceed to find out which of my genes code for cytokine receptors so that I can show on a heat map how their expression varies across clusters. Can any one give me a hint on which tool or method I can use to find out which of my genes code for cytokine receptors? Thanks in advance.

ADD COMMENTlink
0
Entering edit mode

Thank you very múch. I searched the GO term data base for "cytokine receptor activity" and I got this which consists of a set of genes which I can download as an excel file. My next step will be to programmatically match the genes in the excel file to those in my gene list and subset from my list those that are cytokine receptors.

ADD REPLYlink
3
Entering edit mode
14 months ago
United States

I'm sure there are many ways to go about this (including literature research via PubMed), but for a start, you could search the GO term data base, which, for "cytokine activity" returns this, which includes a couple 100 genes.

ADD COMMENTlink
2
Entering edit mode

The GO site has a GO enrichment analysis tool found on their homepage, so you can just pop in your IDs and see the mapped terms. I think you can then filter the dataset to see specific terms. Seems like an easier way than matching up lists. It also has options to export in a range of formats and everyone's favourite graphs, pie charts.

ADD REPLYlink
1
Entering edit mode

that's a good point -- if you already have a list of genes of interest, that would be even more elegant (although it may not hurt to know how many cytokines there are in the set of "non-interesting" genes, but that depends on the precise question)

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.3