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 hypoxia 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_hypoxia(2020)

pdat1 <- lapply(datasets, pdat_hypoxia)
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; Hx48 – hypoxia 48 h; Hx72 – hypoxia 72 h; -S – supernatant fraction; -P – pellet fraction; DMSO – dimethyl sulfoxide; NO.sul – nitric oxide-donating sulindac; sul – sulindac; 4Gy – radiation; POS – primay origin canine osteosarcoma (OS) cells; HMPOS – metastatic origin canine OS cells.
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("hypoxia.csv")
write.csv(out, file, row.names = FALSE, quote = 2)

Data Sources

Where given, gene names or other identifiers were converted to UniProt accession numbers using the UniProt mapping tool.

a. Supplemental Table 1 of @SBB+06, filtered to include proteins with expression ratio ≥ 1.7 or ≤ 0.58. b. Supplemental Table 2A of @FWH+13 (control virus cells). c. d. Supplemental Table S1 of @RHD+13, filtered to include proteins with iTRAQ ratios < 0.83 or > 1.2 and p-value < 0.05. e. Supporting Information table of @VTMF13, filtered to include proteins with a normalized expression ratio of > 1.2 or < 0.83. f. Supporting Information Table S1 @DCH+14. g. h. i. j. Supplemental Table S1 of @DYL+14, filtered to include proteins with p-value < 0.05 (-S: supernatant fraction; -P: pellet fraction). k. Supplementary Table S1 of @BSA+15. l. Supplemental Information Table S1 of @HWA+16, filtered to include proteins with a fold change of < 0.5 or > 1 and that were detected in only hypoxic or only normoxic conditions. m. Gene names from @LCS16 (data files provided by Ming-Chih Lai). n. Extracted from Table S2E (whole cell lysate) of @CGH+17, keeping proteins with FDR < 0.05. o. Supplemental Table S4 of @ZXS+17. p. Supplementary Tables S6-S7 (proteome) of @CLY+18. q. List of up- and down-regulated proteins from @GBH+18 (provided by Alex Greenhough), filtered to include proteins with average fold change ≥ 1.5 or ≤ 2/3. r. Gene names from Figure 1F of @LKK+18. s. Supplemental file 1 of @WTG+18 (provided by Gordana Vunjak-Novakovic), filtered to include proteins with Normalized Ratio [Hypoxia MSC/Control MSC] ≥ 1.5 or ≤ 2/3 and p-value < 0.05. t. Gene names from Supplementary file S1 of @CSK+19 for the two replicates labelled as "input_Log2ratioHL_firstIP" and "input_Log2ratioLH_secondIP" (soluble extracts before immunoprecipitation), filtered to include proteins where Log2ratio is > 0.2 or < -0.2 for both replicates. u. v. Supplementary Data 1 of @GPT+19, filtered to include proteins with p-value < 0.05 and fold-change > 2 or < 0.5 w. Proteins identified as up- or down-regulated > 1 SD in Data File S1 of @KAN+19 (sheet "Proteome"). x. Additional file 1: Table S1 of @LLL+19. y. Gene names from Supplementary Information Tables S6 and S7 of @BCMS20. z. A. B. C. D. E. Supplementary Table 1A of @RVN+20, filtered to include proteins with median fold change between normoxic and hypoxic conditions in any individual treatment > 1.5 or < 2/3. F. G. Supplementary Tables S3b (sheet "HPNP") and S3c (sheet "HHNH") of @SPJ+20.