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 3D compared to 2D culture 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_3D(2020)

pdat1 <- lapply(datasets, pdat_3D)
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; P2 – passage 2; P5 – passage 5; MSC – mesenchymal stromal 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("3D.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. Gene names from Supporting Information Table 1S of @PLC+10. b. c. Sheets 2 and 3 in Table S1 of @MHG+12. d. e. Supplemental Table 1C of @MVC+12, filtered to include proteins with expression ratios < 0.77 or > 1.3. f. Supplemental Table S5 of @YYW+13. g. h. Supplemental Table S4 of @ZMH+13. i. Table S1 of @HKX+14. j. k. l. Supplemental Table S1 of @KDS+14 (hESC: human embryonic stem cells; hiPSC: human induced pluripotent stem cells; hPSC: human pluripotent stem cells). m. Table S2 of @RKP+14, filtered to include proteins that have differences in spectral counts recorded in at least two of three experiments, absolute overall fold change is ≥ 1.5 or ≤ 2/3, and p-value is < 0.05. n. Supplementary Figure 2 of @SAS+14. o. P1_Data sheet in the Supporting Information file of @WRK+14. p. Supplemental Table S1 of @MTK+15, filtered to exclude marked contaminants and reverse sequences and to include proteins with "Ratio H/L normalized" > 1.5 or < 2/3. q. Tables S1a and S1b of @YLW+16. r. Tables S2 and S3 of @KJK+18. s. t. Supplementary Table 3 of @TGD18. u. Extracted from proteinGroups.txt in ProteomeXchange Dataset PXD008244/txt.zip [@EWK+19], including proteins quantified in at least two replicates in each condition (adherent and spheroid) and with median fold change > 2 or < 0.5. v. Extracted from Supplementary Table 1 of @GADS19. Values were quantile normalized, then ratios were calculated between 3D and 2D cultures for each treatment (control, CBD, UVA, UVA+CBD, UVB, UVB+CBD). Ratios > 1.2 or < 1/1.2 in at least 4 treatments were used to identify differentially expressed proteins. w. Supplementary Data I, sheet "Volcano plot 2Dv3D" of @HLC19. x. y. z. Supporting Table 1 of @LPK+19, sheets "3P2P" (mono-cultured preadipocytes), "3A2A" (mono-cultured adipocytes), "3C2C" (co-cultured adipocytes with macrophages), filtered to include proteins marked as "T-test Significant" and with absolute value of "N: T-test Difference" > log~2~(0.5). A. Supplementary Table S2 of @DKM+20, filtered to include proteins with fold change > 2 or < 0.5 for all donors.

References

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