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

library(JMDplots)
library(knitr)
## use pngquant to reduce size of PNG images
knit_hooks$set(pngquant = hook_pngquant)
pngquant <- "--speed=1 --quality=0-25"
# in case pngquant isn't available (R-Forge?)
if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL 

This vignette from the R package JMDplots version r packageDescription("JMDplots")$Version shows chemical metrics for proteins that are differentially expressed in high-glucose compared to control conditions. The analysis is described in more detail in a paper (Dick, 2021). Abbreviations:

• Z_C – average oxidation state of carbon.
• n_H2O – stoichiometric hydration state per residue (Dick et al., 2020) computed using the QEC basis species (glutamine, glutamic acid, cysteine, H~2~O, O~2~).

datasets <- pdat_glucose(2020)

pdat1 <- lapply(datasets, pdat_glucose)
comptab1 <- lapply(pdat1, get_comptab)
comptab2 <- lapply(pdat1, get_comptab, "nAA", "MW")

Differences are calculated as (median value for up-regulated proteins) - (median value for down-regulated proteins). Dashed lines enclose the 50% confidence region for highest probability density.

par(mar = c(4, 4, 1, 1))
diffplot(comptab1, labtext = NA)

In the table, values of ΔZ_C and Δn_H2O are multiplied by 1000, values of ΔMW are multiplied by 100, and negative values are shown in bold. Abbreviations:

• n~down~ – number of down-regulated proteins; n~up~ – number of up-regulated proteins; HUVEC – human umbilical vein endothelial cells; eMP – endothelial-derived microparticles.
• n_AA – protein length; MW – molecular weight per residue.

library(xtable)
out <- xsummary2(comptab1, comptab2)
# round values and include dataset tags
tags <- sapply(sapply(strsplit(datasets, "="), "[", -1), paste, collapse = ";")
out <- cbind(out[, 1:2], tags = tags, out[, 3:16])
out[, 6:17] <- round(out[, 6:17], 4)
file <- paste0("glucose.csv")
write.csv(out, file, row.names = FALSE, quote = 2)

Data Sources

a. b. c. Supporting Information Table of @PW08, filtered to include proteins with expression ratios < 0.9 or > 1.1 and with p-values < 0.05. d. Supplemetary Table ST4 of @WCM+09, filtered to include the proteins with ANOVA p-value < 0.01 (red- and blue-highlighted rows in the source table), 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. Supplementary Table of @WFSL09, filtered to include proteins with fold change > 1.2 or < 0.8. f. Table 1 of @MFD+10. g. h. Table 1 of @CCC+12. i. Proteins identified as differentially abundant in Supporting Information Table S5 of @SFG+12, filtered to include proteins with fold change > 2 or < 0.5. j. k. Table 1 of @CCCC13. l. Supplementary Table 1 of @CCW+13, filtered to include proteins with average fold change > 2.5 or < 0.4. m. Supporting Information Table S4 of @LDB+15 for up- (Cluster 1) and down- (Cluster 5) regulated proteins. n. o. Electronic supplementary material Table 1 of @BTX+17. p. q. Supplementary Table S1 of @SFKD17, filtered to include proteins with fold change > 2 or < 0.5 (ratios were computed from medians of iBAQ values for three replicates after quantile normalization). r. Supplementary Tables 1 and 2 of @IXA+19. s. t. Supplementary Table 2 of @MHP+20 (sheets "H9c2" and "HEK"). u. v. w. x. Treatment with high glucose (12.5 mmol/L) or high mannitol (7.0 mmol/L + 5.5 mmol/L glucose) followed by insulin, compared to normal glucose (5.5 mmol/L) followed by insulin. Source: Supplementary Tables S2--S6 of @MPR+20 (proteins uniquely identified in treatment and control conditions).

References

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