Question: Is there a data base, tool or method I can use to find out which of my genes code for cytokine receptors?
0
gravatar for charlesgwellem
4 weeks ago by
charlesgwellem0 wrote:

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.

R rna-seq genome gene • 162 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by charlesgwellem0

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 written 4 weeks ago by charlesgwellem0
3
gravatar for Friederike
4 weeks ago by
Friederike3.3k
United States
Friederike3.3k wrote:

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 written 4 weeks ago by Friederike3.3k
2

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 written 4 weeks ago by Erin_Ensembl310
1

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 written 4 weeks ago by Friederike3.3k
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