---
title: "Hyperosmotic Stress"
output:
rmarkdown::html_vignette:
mathjax: null
vignette: >
%\VignetteIndexEntry{Data: Hyperosmotic Stress}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
bibliography: data_sources.bib
csl: peerj.csl
---
This [vignette](http://chnosz.net/canprot/doc/index.html) from the R package [canprot](http://github.com/jedick/canprot) reproduces calculations of compositional oxidation state and hydration state that are described in a paper published in _PeerJ_ ([Dick, 2017](https://doi.org/10.7717/peerj.3421)).
## Abbreviations
VHG (very high glucose), ARPE-19 (human retinal pigmented epithelium cells), ECO57 (_Escherichia coli_ O157:H7 Sakai), IOBA-NHC (human conjunctival epithelial cells), CAUCR (_Caulobacter crescentus_), tr. (transcriptome), pr. (proteome), CHO (Chinese hamster ovary cells).
## Summary Table
This table compares the chemical compositions of groups of proteins that are relatively down- and up-expressed (`n1` and `n2`, respectively) in cells grown in hyperosmotic stress compared to control conditions.
```{r options, echo=FALSE}
options(width = 90)
```
```{r canprot, message=FALSE}
library(canprot)
```
Get datasets considered in [Dick, 2017](https://doi.org/10.7717/peerj.3421) and [Dick et al., 2019 (preprint)](hyperosmotic.html)
```{r pdats, message=FALSE}
datasets <- pdat_osmotic()
pdat <- lapply_canprot(datasets, get_pdat, pdat_fun = "pdat_osmotic")
datasets2 <- pdat_osmotic2()
pdat2 <- lapply_canprot(datasets2, get_pdat, pdat_fun = "pdat_osmotic2")
```
Put the datasets together.
Remove this step to make the plot as in Dick, 2017.
```{r pdat, message=FALSE}
datasets <- c(datasets, datasets2)
pdat <- c(pdat, pdat2)
```
Make the table of compositional metrics (carbon oxidation state and stoichiometric hydration state).
```{r comptab, message=FALSE}
comptab <- lapply_canprot(pdat, get_comptab, plot.it = FALSE)
```
```{r xsummary, results="asis"}
library(xtable)
xsummary(comptab)
```
## Data Sources
a. b. c. VHG (300 g/L) vs control (20 g/L). The comparisons here use proteins with expression ratios < 0.9 or > 1.1 and with p-values < 0.05. Source: SI Table of @PW08.
d. 24 h at 16.7 mM vs 5.6 mM glucose. Source: extracted from Suppl. Table ST4 of @WCM+09; including the red- and blue-highlighted rows in the source table (those with ANOVA _p_-value < 0.01), and applying the authors' criterion that proteins be identified by 2 or more unique peptides in at least 4 of the 8 most intense LC-MS/MS runs.
e. 300 mOsm (control) or 400 mOsm (NaCl treatment). Source: Suppl. Table 1 of @OBBH11.
f. g. Mannitol-balanced 5.5 (control), 25 or 100 mM ᴅ-glucose media. Source: Table 1 of @CCC+12.
h. i. j. k. Temperature and NaCl treatment (control: 35 °C, aw = 0.993). Source: Suppl. Tables S13–S16 of @KKG+12.
l. m. 5.5 (control), 25 or 100 mM ᴅ-glucose. Source: Table 1 of @CCCC13.
n. Gill proteome of Japanese eel (Anguilla japonica) adapted to seawater or freshwater. Source: Protein IDs from Suppl. Table 3 and gene names of human orthologs from Suppl. File 4 of @TSZ+13.
o. p. q. 30 min in YNB (2% glucose) vs YPKG (0.5% glucose) media. Source: extracted from Suppl. Files 3 and 5 of @GSC14, using the authors' criterion of _p_-value <0.05.
r. 280 (control), 380, or 480 mOsm (NaCl treatment) for 24 h. Source: Table 2 of @CLG+15.
s. t. u. v. Overnight treatment with a final concentration of 40/50 mM NaCl or 200 mM sucrose vs M2 minimal salts medium plus glucose (control). Source: Additional file Table S2 of @KLB+15.
w. x. 15 g/L vs 5 g/L (control) glucose at days 0, 3, 6, and 9. The comparisons here use all proteins reported to have expression patterns in Cluster 1 (up) or Cluster 5 (down), or only the proteins with high expression differences (ratio ≤-0.2 or ≥0.2) at all time points. Source: SI Table S4 of @LDB+15.
y. 4.21 osmol/kg vs 3.17 osmol/kg osmotic pressure (NaCl treatment). Source: Table 1 of @YDZ+15.
z. 0.1 M KCl (treatment) vs medium with no added KCl (control). Source: Suppl. Tables 2 and 3 of @RBP+16.
A. B. Tables 1 and 2 of @LRB+09.
C. Supplementary Table 8 of @FTR+10. Only proteins with consistent expression ratios (all > 1 or all < 1) at each time point (15, 60, and 180 min.) were included.
D. E. Supplementary Tables 2 (membrane proteomics) and 3 (transcriptomics) of @HMO+10. The cytosol proteomics experiment was not included because of the low number of proteins identified with a significant expression difference. Only proteins with consistent expression ratios in at least 3 of 4 time points (10, 30, 60, and 120 min.) were included.
F. G. Table S-1 of @ZLZ+16. Values of reporter intensities at each condition (6%, 10%, and 17.5% NaCl) were normalized to a mean of 1; normalized values were used to compute intensity ratios (10% / 6% NaCl and 17.5% / 10% NaCl). Only proteins with expression ratios > 1.3 in either direction [@ZLZ+16], p-values < 0.05, and at least 2 peptides were included.
H. I. Tables S2 and S3 of @LLYL17.
J. K. Tables S1–S6 of @LJC+18. For each of the wild-type and ∆*sigB* mutant, only proteins that were identified in multicellular vesicles in a single condition (0.5 M salt stress or without salt stress) were included.
L. M. Supporting Table 1C of @JSP+19. Only proteins with at least 2-fold expression difference and marked as significant were included.
## Mean Differences
The dataset for adipose-derived stem cells is highlighted in orange.
```{r diffplot, fig.width=6, fig.height=6, fig.align="center"}
col <- rep("black", length(datasets))
col[grepl("=ASC", datasets)] <- "orange"
diffplot(comptab, col = col, oldstyle = TRUE)
```
## References