In jedick/JMDplots: Plots from Papers by Jeffrey M. Dick

This vignette from the R package JMDplots version r packageDescription("JMDplots")$Version approximately reproduces calculations of compositional oxidation state and hydration state that are described in a paper published in PeerJ (Dick, 2017). The reproduction is not exact because of data updates made in the package after the paper was published.

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.

options(width = 90)

library(canprot)

datasets <- .pdat_osmotic(2017)
pdat <- lapply(datasets, .pdat_osmotic)

comptab <- lapply(pdat, get_comptab, plot.it = FALSE, mfun = "mean", oldstyle = TRUE)

library(xtable)
out <- xsummary(comptab)
# round values and include dataset tags
tags <- sapply(sapply(strsplit(datasets, "="), "[", -1), paste, collapse = ";")
out <- cbind(out[, 1:2], tags = tags, out[, 3:14])
out[, 6:15] <- round(out[, 6:15], 4)
write.csv(out, "hyperosmotic.csv", row.names = FALSE, quote = 2)

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, a_w = 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.

Mean Differences

The dataset for adipose-derived stem cells is highlighted in orange.

col <- rep("black", length(datasets))
col[grepl("=ASC", datasets)] <- "orange"
diffplot(comptab, col = col, oldstyle = TRUE)

References

jedick/JMDplots documentation built on April 12, 2025, 1:35 p.m.