| li2017 {isotracer} | R Documentation |
Protein degradation in Arabidopsis plants (Li et al. 2017)
Description
Dataset built from the Dryad depository entry associated with the article "Protein degradation rate in Arabidopsis thaliana leaf growth and development" by Li et al. (2017)
Usage
li2017
Format
li2017 is the main dataset and is a tibble with columns:
- prot_id
Protein identifier. Can be matched to a more explicit protein description in
li2017_prots.- sample
Sample identity. Different samples were used for relative abundance measurements and labelled fraction measurements.
- rel_abundance
Relative abundance compared to a reference sample.
- labeled_fraction
Proportion of 15N in the protein.
- time_day
Time elapsed since growth medium switch to 15N, in days.
- leaf_id
Leaf identity (3rd, 5th, or 7th leaf of individual plants).
li2017_prots maps protein identifiers to protein descriptions
and is a tibble with columns:
- prot_id
Protein identifier. Can be matched with the same column in
li2017.- description
Protein description
li2017_counts is a summary table counting the number of
available data points for relative abundance and labelled fraction for
each protein in li2017. It is a tibble with columns:
- prot_id
Protein identifier. Can be matched with the same column in
li2017.- n_abundance_data
Number of relative abundance data points for a given protein.
- n_labelling_data
Number of labelled fraction data points for a given protein.
Details
In this study, the authors used a growth medium containing 15N to grow 21-day old Arabidopsis plants which were grown on a natural 14N/15N medium until that day. The third, fifth and seventh leaves were sampled from individuals at different time points after the medium switch (0, 1, 3 and 5 days). Proteins were identified and labelled fractions were measured using mass spectrometry. Relative protein abundances were determined in comparison with a reference sample.
The aim of the authors was to quantify in vivo degradation rates for as many proteins as possible (1228 proteins in the original paper) and examine which determinants had an effect or not on protein degradation rates (e.g. protein domains, protein complex membership, ...).
Three datasets were extracted from the large dataset available on Dryad for
packaging inside isotracer: li2017, li2017_prots, and
li2017_counts.
Source
Data was taken from the following Dryad repository: Li, Lei, Clark J. Nelson, Josua Troesch, Ian Castleden, Shaobai Huang, and A. Harvey Millar. “Data from: Protein Degradation Rate in Arabidopsis Thaliana Leaf Growth and Development.” Dryad, 2018. https://doi.org/10.5061/DRYAD.Q3H85.
The Dryad repository was associated with the following paper: Li, Lei, Clark J. Nelson, Josua Trösch, Ian Castleden, Shaobai Huang, and A. Harvey Millar. “Protein Degradation Rate in Arabidopsis Thaliana Leaf Growth and Development.” The Plant Cell 29, no. 2 (February 1, 2017): 207–28. https://doi.org/10.1105/tpc.16.00768.