Question: Identifying Genes That Express Different Isoforms In Cancer Vs Normal Rna-Seq Data
1
gravatar for Sahel
7.4 years ago by
Sahel250
CANADA
Sahel250 wrote:

Hi There,

I am trying to find genes that express different isoforms in cancer vs normal RNA-seq data. The first thing that came to my mind was to do a differential expression analysis at exon level (I used edgeR for this)... then if I find a gene that express less number of exon compared to the annotation data for that gene, it means the gene is expressing a different isoform in cancer.

But this is clearly not the right way to do this, and I could not find any other way for this kind of analysis. I was wondering if someone has done this kind of analysis before can share his/her experience with me.

I really appreciate your help, Thanks, Sahel

splicing expression isoform • 3.6k views
ADD COMMENTlink modified 2.5 years ago by kristoffer.vittingseerup2.9k • written 7.4 years ago by Sahel250
2
gravatar for Ahmetz
7.4 years ago by
Ahmetz60
New york, NY
Ahmetz60 wrote:

Sahel, you should check you DEXseq package. It is made for detecting differential exon usage and has nice visualizations.

ADD COMMENTlink written 7.4 years ago by Ahmetz60

This is great, thank you so much Ahmet :)

ADD REPLYlink written 7.4 years ago by Sahel250

This is an old thread, but for what it is worth the DEXseq link is now here

ADD REPLYlink written 5.6 years ago by beroe140
1
gravatar for JC
7.4 years ago by
JC9.1k
Mexico
JC9.1k wrote:

Maybe the Tuxedo-toolkit can help you: Bowtie + TopHat (with fusion detection) + Cufflinks (with novel isoforms detection). I will run the same analysis in both samples, then with cuffdiff select the interesting isoforms.

ADD COMMENTlink written 7.4 years ago by JC9.1k

Hi JC, I actually took your advice and started to use Tophat/Cufflink a few weeks ago. I have 15 tumor and 5 matched normals (human RNA-seq). Everything works great except Cuffdiff. Right now I am running Cuffdiff on the merge.gtf file of all 20 samples, but it keeps running out of memory and looks to take weeks to run! (I am using 12 cpus with 50GB RAM). I was wondering if you experience the same thing or I am doing something wrong? I have another 100 sample coming in for this project, however it seems it is impossible to use tophat/cufflink with 100 samples! Thanks very much, :-)

ADD REPLYlink written 6.7 years ago by Sahel250
1

looks like a problem in the cufflinks installation, I didn't see that error in my analysis previously. You already have the assembled GTF, so you can use edgeR or DEXseq with the reads counts if you cannot fix the cuffdiff problem.

ADD REPLYlink written 6.7 years ago by JC9.1k
1
gravatar for kristoffer.vittingseerup
2.5 years ago by
European Union
kristoffer.vittingseerup2.9k wrote:

An alternative IsoformSwitchAnalyzeR ( http://bioconductor.org/packages/IsoformSwitchAnalyzeR/ ) which enables statistical identification of isoform switches with predicted functional consequences where the consequences can be chosen from a long list but includes gain/loss of protein domains, signal peptides changes in NMD sensitivity etc. IsoformSwitchAnalyzeR directly parses RSEM output (also support cufflinks/cuffdiff, Kallisto andSalmon). IsoformSwitchAnalyzeR

Hope this helps

Kristoffer

ADD COMMENTlink written 2.5 years ago by kristoffer.vittingseerup2.9k
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