Question: Ribosomal Profiling Dataset For Analyzing Whether The Gene Is Translating Or Not
gravatar for RT
7.1 years ago by
European Union
RT340 wrote:

Dear All,

I have set of genes for which we want to make sure that these are translating in order to proceed for next step of the experiment. I got few ribosomal profiling datasets for my species (all are microarray except one). If I am not wrong then I should check the intensity values of my genes from the microarray dataset in order to say that set of my genes with intensity above a threshold are translating. Can any one please let me know what would the stringency criteria in this case.

Is there any tool/package for this work? Guidelines to start analyzing these datsets or recommendation of some good papers would also be helpful.

Many thanks, R.

translation • 1.6k views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 7.1 years ago by RT340
gravatar for Sean Davis
7.1 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

In general, thresholds are platform, probe, and experiment specific so you will probably have a difficult time getting a straight answer. That said, if your dataset is large, you could try looking at the per-probe and per-array distributions in comparison to negative controls on the array to try to extract a threshold that makes sense for your platform.

ADD COMMENTlink written 7.1 years ago by Sean Davis25k

Thanks a lot Sean for your answer. Please suggest if we can rely on microarrays in this case or is it mandatory to generate some sequencing dataset for this. Any useful reference?

ADD REPLYlink written 7.1 years ago by RT340

I'd not move ahead with sequencing without analyzing the microarrays first. If it is not clear how to do that, I'd suggest finding a collaborator who has experience with microarray data and work together to answer your questions for your data.

Sequencing is useful, but it is not a panacea and brings with it a whole host of complications and analysis headaches that can often exceed those associated with microarrays.

ADD REPLYlink written 7.1 years ago by Sean Davis25k
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