Ribosomal Profiling Dataset For Analyzing Whether The Gene Is Translating Or Not

Question

[GR]

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.

Answer 1

[Sean Davis]

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.

[GR]

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?

[Sean Davis]

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.