Question: DEXSeq transcripts per condition
0
4.5 years ago by
Austria
peter_venhuizen0 wrote:

Hello,

I'm trying out DEXSeq for the identification of differentially expressed/spliced transcripts in my experiments. Using DEXSeq it is easy to identify the differentially used exons for each gene and by running

plotDEXSeq(dxr, "gene-name", displayTranscripts=T, names=T, legend=T) 

it also possible to identify the transcripts for each gene.

Now, theoretically I would be able to identify which transcripts are present in which condition for each gene, based on these plots. However, this is extremely time consuming (even for all smaller number of genes) and I have to do this for multiple samples and hundreds or maybe thousands of genes. Therefore I was wondering if it is possible to produce a list of transcripts per gene for each condition using DEXSeq. Something like this:

 COND A COND B gene_A gene_A.1 gene_A.2 gene_A.1 gene_B gene_B.2 gene_B.1 gene_B.3 ... ... ... gene_N gene_N.1 gene_N.2

which gives an easy overview of the transcripts expressed in each condition.

Peter Venhuizen

dexseq transcripts isoforms • 713 views
modified 4.4 years ago by Alejandro Reyes1.7k • written 4.5 years ago by peter_venhuizen0

I am also looking for the same type of analysis. Did you find the solution for this?

1
4.4 years ago by
Alejandro Reyes1.7k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.7k wrote:

Hi Peter,

You can find the information of which transcripts overlap with each exonic bin in the annotation columns of the DEXSeqDataSet object.

rowRanges(dxd)\$transcripts

DEXSeq will give you exons that are differentially used and it usually does not provide information about which isoforms are expressed or which isoforms are not expressed. But if you are concluding this by evaluating visually the DEXSeq plots, it also sounds like something that could be automated. Could you expand of how are you doing this based on the plotDEXSeq outputs?

Alejandro