I’m working with non coding rna to see their expression with ageing, i did differential analysis using deseq2 and got the ncRNA and protein coding genes, now I wanted to see the coexpression of ncRNA with coding genes, how do I do that? I’m new to bioinformatics so finding it really difficult, any help will be really appreciated. Thank you
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written
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gulamaltab •
1 answer
Just create a co-expression network using both coding and non-coding genes, and then explore the relationships between these via, for example, community structure: Network plot from expression data in R using igraph
Alernatively, if you use WGCNA, you can explore the relationships based on membership to particular modules.
A 'co-expression' network, remember, is just a way to summarise correlations between your variables or samples. Network analysis has fans and has enemies. I am yet to see how it has shaped hypotheses / conclusions in any major way.
A good read for you, recommended by an Italian colleague of mine: Gene co-expression analysis for functional classification and gene-disease predictions.
Kevin
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