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RUST for dwell time
27-Jul-2017, 10:08 AM
Post: #4
RE: RUST for dwell time
(20-Jul-2017 01:09 PM)Amire Wrote:  1. To what extent do you think this value indeed relates to dwell time. meaning what is it ignoring or assuming.

Most of normalization approaches would give a reasonable estimation of relative dwell times if data were ideal as evident from simulations. RUST advantage is its resistance to noise in comparison with other methods. It seems that there is a lot of noise in the ribo-seq data for various reasons (both biological and technical), so foremost RUST is intended to be practical. The transformation that provides robustness to RUST, however, results in the loss of some useful information. One problem that is associated with that is that RUST consistently overestimates the dwell times of the quickest codons. In other words, the smallest relative dwell times are likely to be even smaller than it is estimated with RUST.

(20-Jul-2017 01:09 PM)Amire Wrote:  2. is there a different normalization or a different strategy you would consider in order to look for change in dwell time between samples rather than comparing codons within one sample?

We haven't perform a comparison of approaches for this purpose, it seems that this is simple to achieve as evident from numerous publications where synthesis of specific amino acids was impaired. Perhaps RUST advantage would be less obvious when you compare two datasets obtained from the same biological sample and under the same protocol, as the noise would be similar. But I suspect that RUST could be used for this purpose as well.

(20-Jul-2017 01:09 PM)Amire Wrote:  3. it seems that the governing parameter in this plot is the amino acid and not the codon. As if the limiting step is the supply of amino acids. is this indeed the case?

The data are plotted for amino acids on axis x and this is done primarily for convenience. In some cases the variation in dwell times of synonymous codons for a specific amino acids seems substantial. But we do not know how well these data reflect the reality, for example because CHX have a preference for blocking certain codons, see Figure 5 in Lareau et al paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4052883/. It is possible that CHX preferentially acts on amino acids rather than codons, perhaps this was even addressed already and the answer could be found in the literature.

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Messages In This Thread
RUST for dwell time - Amire - 20-Jul-2017, 09:23 AM
RE: RUST for dwell time - Patrick O' Connor - 20-Jul-2017, 12:45 PM
RE: RUST for dwell time - Amire - 20-Jul-2017, 01:09 PM
RE: RUST for dwell time - First citizen of GWIPS - 27-Jul-2017 10:08 AM

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