Extracting transcriptonally perturbated gene subnetworks using a list of target genes, RNA-Seq data and pathway informations

Question

[Nicolas Rosewick]

Hi,

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 ?

Thanks

[biogirl]

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

[Nicolas Rosewick]

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

[biogirl]

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: http://www.gettinggeneticsdone.com/2012/03/pathway-analysis-for-high-throughput.html