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 secreted 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_secreted(2020)

pdat1 <- lapply(datasets, pdat_secreted)
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; pMSC – placental mesenchymal stem 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("secreted.csv")
write.csv(out, file, row.names = FALSE, quote = 2)

Data Sources

Gene names or other identifiers were converted to UniProt accession numbers using the UniProt mapping tool.

a. Tables 2 and 3 of @BRA+10. b. c. Gene names from Supplementary Table S1 of @PTD+10, filtered with p-value < 0.05, expression ratio > 1.3 or < 1/1.3 and EF < 2. d. Extracted from Supplementary Table SIII of @JVC+12: median values of peptide quantification (omitting proteins identified with less than 5 peptides that have different signs of log~2~ values); differentially expressed proteins identifed using a log~2~ cutoff of 0.2. e. Extracted from Table 1 of @SKA+13, to include proteins exclusively identified in 1% or 8% O~2~. f. g. Extracted from Table 1 of @SRS+13a, including unique proteins for 1%, 3%, and 8% O~2~. h. GI numbers from Supplementary Data 6 of @LRS+14. i. j. Extracted from Table S1 of @YKK+14, to include proteins identified by at least 2 unique peptides and surpassing a log~2~ cutoff of 0.5 in soluble or exosome fractions. k. l. Gene names from Supplementary Information Table 1 of @CRS+15, filtered to include proteins with log~2~ fold change between air and hypoxia > 0.2 or < -0.2. m. Gene names from Supporting Information Tables S1 (normoxic) and S2 (hypoxic) of @RTA+15, filtered to include proteins that were exclusively identified in either condition. n. Gene names from Tables 1 and 2 of @RSE+16. o. p. Extracted from Tables S2A (exosomes) and S2B (secretome) of @CGH+17, keeping proteins with FDR < 0.05. q. Supplementary Tables S8-S9 (secretome) of @CLY+18. r. Supplementary Table 1 of @DWW+18. s. Table S2 of @FPR+18. t. Supplementary Material Tables S1 and S2 of @ODS+18, filtered to include proteins exclusively identified in hypoxia or normoxia. u. Supplementary Tables 1 and 2 of @CWG+19, filtered to include proteins uniquely identified in either hypoxia or normoxia. v. Proteins identified as up- or down-regulated > 1 SD in Data File S1 of @KAN+19 (pooled data from sheets "Soluble Secretome" and "EVs"). w. x. Extracted from proteinGroups.txt in ProteomeXchange Dataset PXD008104 [@NJVS19]. Expression ratios between hypoxia and normoxia were calculated from LFQ intensity values, and proteins were classified as up- or down-regulated if they had expression ratios > 1.2 or < 1/1.2 in all three experiments for one cell type (CAM or NTM). The Majority protein IDs and mean values of the expression ratios were saved in the data file. y. Supplementary Table 2 of @PDT+19, filtered with log~2~ fold-change cutoff of 1.

References

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