How can I identify inflammatory genes from the Molecular signature database?

Question

[Jaber]

Hi Biostars,

I read recently an abstract, that said they identified inflammatory genes from the molecular signature database. I am struggling to identify the inflammatory genes.

The link to the paper: https://ascopubs.org/doi/10.1200/JCO.2024.42.3_suppl.551

The code I use, please correct me if I am wrong:

msigdbr_inf <- msigdbr(species = "Homo sapiens", category = "C7")

msigdbr_inf <- msigdbr_inf %>% 
  filter(.$gs_subcat == "IMMUNESIGDB")

I appreciate your help.

Answer 1

[GenoMax]

https://www.gsea-msigdb.org/gsea/msigdb/cards/HALLMARK_INFLAMMATORY_RESPONSE

Click on the Show members link to see the genes. There are 200.

[Jaber]

Many thanks!

Really appreciate it.

Answer 2

[ATpoint]

Inflammation is a vague term. Is it programmed cell death, or interleukin signaling, or response to bacterial antigens, or NLRP3 activation, or one of many others? You need to define the term based on your knowledge of the biological system to make sense out of such terms. Our group works fulltime on inflammatory processed and I have yet to see the one single term that reliably describes inflammation as such simple because the process is so diverse and the word is loosely defined.

[Jaber]

Thank you for your valuable advice. I appreciate the complexity and diversity of inflammation as a biological process. I will definitely work to be more specific in my definitions and ensure that I convey the nuances associated with various aspects of inflammation in my future work.