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 hyperosmotic compared to control conditions. The analysis is described in more detail in a paper (Dick et al., 2020). 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~).
• pI – isoelectric point; GRAVY – grand average of hydropathicity.
• n_AA – protein length; MW – molecular weight per residue.

datasets <- pdat_osmotic_bact(2020)

pdat1 <- lapply(datasets, pdat_osmotic_bact)
comptab1 <- lapply(pdat1, get_comptab)
comptab2 <- lapply(pdat1, get_comptab, "pI", "GRAVY")
comptab3 <- 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.

layout(matrix(c(0, 2, 1, 2, 1, 3, 0, 3), nrow = 2))
par(cex = 1, mar = c(4, 4, 1, 1), mgp = c(2.5, 1, 0))
diffplot(comptab1, labtext = NA)
diffplot(comptab2, c("pI", "GRAVY"), labtext = NA)
diffplot(comptab3, c("nAA", "MW"), labtext = NA)

In the table, values of ΔZ_C, Δn_H2O, and ΔGRAVY are multiplied by 1000, values of ΔpI and 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; aw – water activity; LB – lysogeny broth; WT – wild-type; MMO – medium minus osmoprotectants.

library(xtable)
out <- xsummary3(comptab1, comptab2, comptab3)
# round values and include dataset tags
tags <- sapply(sapply(strsplit(datasets, "="), "[", -1), paste, collapse = ";")
out <- cbind(out[, 1:2], tags = tags, out[, 3:19])
out[, 6:20] <- round(out[, 6:20], 4)
file <- paste0("osmotic_bact.csv")
write.csv(out, file, row.names = FALSE, quote = 2)

Data Sources

a. Additional file 3: Table S2 of @PNWB09. b. 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. c. Supporting Information Table 1 of @LPK+13 (sheets "Up-Down Proteins" and "Unknown function"). d. e. Supplementary Tables S3A and S3B of @QHT+13. f. Table 1 (proteins) and supplemental Table S2 (genes) of @ADW+14. g. h. i. j. Supporting Information Table S2 of @KKG+14. k. l. Supporting Information Table of @PBP+14, filtered to include proteins with p-value < 0.05. m. n. Additional file Table S2 of @KLB+15. o. p. Supplementary Table S6 of @SKV+16, filtered to include proteins with fold change > 2 or < 0.5 for the ratios Glucose / LB (lysogeny broth) or Osmotic-stress glucose / LB. q. Supplementary Table 1 (sheets "0.76 fold down regulated" and "1.3 fold up regulated") of @KAK+17. r. Supplemental Table S-2 of @LYS+17, filtered to include proteins with log~2~ fold change > 1 or < -1 and p-value < 0.05. s. Supplementary Figure 1 of @HGC+18. t. Supplementary Table 1 of @KSK+18 (amino acid compositions computed from protein sequences in the list of gene annotations). u. v. 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. w. x. Extracted from proteinGroups.txt in PRIDE project PXD010072/MaxQuantOutput.tar.gz [@TSC18], filtered to include proteins with non-zero LFQ intensity values for all replicates in each experiment; the medians of these values were used to compute fold changes; proteins with fold change > 1.5 or < 2/3 were kept. y. Table 2 of @LWS+19. z. A. Supplementary Tables S4 and S5 of @MGF+19, filtered to include proteins with fold change >= 2 or <= 0.5. B. Supplementary Table 1 (sheets ">2.0 Fold" and "< 0.5 Fold") of @AST+20. C. D. Supplementary Table 1 of @GBR+20 (column "MMO+NaCl/MMO" for CIRM129 and CIRM1025).

References

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