Question: Differentially Expressed Genes In Highly Correlated Samples?
gravatar for Pfs
9.1 years ago by
United States
Pfs510 wrote:

I have an RNASEQ experiment with 6 samples (3 treatments and 3 corresponding controls, i.e. A,B,C and ctrlA, ctrlB, ctrlC).

I used cuffdiff to determine the differentially expressed genes/isoforms for the 3 comparison: A vs ctrlA, B vs ctrlB, C vs ctrlC and got some sets of interesting genes/isoforms.

When I compute the correlation between the samples and then clustering, I was expecting to see either the treatments clustering with their corresponding control or clustering together but separately from the control. Instead they all have high correlation > 0.98 with each other (treatment and control).

Is it possible to have DE genes among samples that are highly correlated? My first interpretation would be that the genes have a different expression magnitude across samples, but their trend is conserved across sample. Is this correct? What can I do to further test the data?

Thanks in advance

gene correlation rna • 2.9k views
ADD COMMENTlink modified 8.8 years ago by Damian Kao15k • written 9.1 years ago by Pfs510
gravatar for Damian Kao
9.1 years ago by
Damian Kao15k
Damian Kao15k wrote:

It is possible to have DE genes among samples that are highly correlated. Some treatments just don't cause a wide-spread change in gene expression.

A short answer would be to do replicates to give you more statistical power on the DE genes.

A few things you can ask yourself:

  • Was there a positive control in your treatments? I am assuming there is something interesting about this treatment that made you want to RNA-seq it in the first place. When you made your libraries, did you have a positive control to make sure your treatment worked?

  • Do you have any genes or qPCR-ed genes that are known to be down/up regulated after the treatment? You can compare your results and see if they match.

  • How did you map and calculate the expression levels? Did you use RPKM or tags for the DE analysis?

  • Did you ribo-deplete the libraries? What is your estimated coverage of the transcriptome?

ADD COMMENTlink modified 9.1 years ago • written 9.1 years ago by Damian Kao15k

IMHO, a bit of formatting will further enhance the readability of this excellent answer.

ADD REPLYlink written 9.1 years ago by Khader Shameer18k
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