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.

  • $\begingroup$ So you're saying you want to convert the gene IDs to gene symbols such as IL15RA? R script typically works $\endgroup$ – CKM Feb 21 '19 at 19:24
  • $\begingroup$ As pointed out by @CKM, this is a simple case of finding the gene name corresponding to the ids used in the sequencing analysis. It's quite straightforward if you have a table of gene ids and corresponding names. You can do it manually for a small set of genes or use a simple script in your favorite programming language for parsing the names. $\endgroup$ – WYSIWYG Feb 21 '19 at 22:27

I'm sure there are many ways to go about this (including literature research via PubMed), but for a start, I searched the GO term data base which, for the search term "cytokine receptor activity" returned this, which includes a number of genes which I can download as an excel file and match them with my gene set using R.

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  • $\begingroup$ You stole this answer from someone who answered you on Biostars. biostars.org/p/365294 Are you going to give yourself the best answer points now? $\endgroup$ – swbarnes2 Feb 22 '19 at 17:46
  • $\begingroup$ @swbarnes2: I asked the question on both fora and I want to share what I learned from another forum on this forum. This is because the answers I got on this forum did not directly meet my needs but I do appreciate the responses I got here. Is it a crime? By the way I slightly modified the response suggested to suit my needs. $\endgroup$ – Charles Feb 22 '19 at 22:17

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