Subsetting Common Differentially Expressed Genes in Multigrade Glioma
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22 days ago
mehdim • 0

Hello!

So I am working on reconstructing a gene regulatory network for Glioma/Glioblastoma starting from RNA-seq data. the data I have is for different patients at different stages of the disease (different grades 2, 3 and 4).

I ran a differential expression analysis and extracted the DE genes in-between the different grades. (instead of disease vs control, I ran DESEq2 with the grade as the factor) ie. grade 4 vs grade 2, 3 vs 2 and 4 vs 3.

I got the following results:

The number of DE genes found in between the grades

I want to make sure that it makes sense to take a subset of common genes like this for the purpose of reconstructing a regulatory network, and if the numbers I have are logical in this context.

N.B: The 8 genes from the subset do seem to have a relationship with the disease from the literature, although there is no direct regulation or signaling pathway between them.

Thank you!

regulatory expression differential glioma network rna-seq gene • 170 views
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Seems to me the other thing you could do is do pathway analysis for each set of genes, see if the same pathways come up.

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