Question: Extracting transcriptonally perturbated gene subnetworks using a list of target genes, RNA-Seq data and pathway informations
gravatar for Nicolas Rosewick
5.1 years ago by
Belgium, Brussels
Nicolas Rosewick8.9k wrote:


I've a list of genes (~100) that are mutated in my trated samples compared to untreated. I've also RNA-Seq data from these samples. Now I want to know the potential effect of these mutations on gene expression of direct and indirect target genes of my list of mutated genes. My idea was to use pathway information to check the expression of direct targets of my 100-mutated-genes and check if they are up/down regulated.. My final aim is to detect specific target genes and biological pathways that are perturbated due to the mutateted genes.

Any advice or ideas ?


rna-seq subnetwork pathway • 1.3k views
ADD COMMENTlink written 5.1 years ago by Nicolas Rosewick8.9k

Is the RNAseq data at one time point or a time course?

ADD REPLYlink written 5.1 years ago by biogirl190

it's one time point. It would be better to say disease vs healthy , and not treated vs untreated in my description

ADD REPLYlink written 5.1 years ago by Nicolas Rosewick8.9k

Ok, if you're looking at humans, I'd say try ConsensusPathDB.  If not, perhaps something like MapMan or gene2pathway would do the trick.  Stephen Turner wrote a good blog post on pathway analysis here:

ADD REPLYlink written 5.1 years ago by biogirl190
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