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 breast cancer compared to normal tissue. 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_breast(2020)

pdat1 <- lapply(datasets, pdat_breast)
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; T – tumor; N – normal; LCM – laser capture microdisecction; FFPE – formalin-fixed paraffin-embedded; IDC – infiltrating ductal carcinoma; DCIS – ductal carcinoma in situ; TNBC – triple-negative breast cancer.
• 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("breast.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. Extracted from Supporting Information RTF files of @AMG+08. Proteins identified by any number of peptides in both cancer and matched periphery were excluded; of the remaining proteins those identified by at least two peptides were used. b. Table S2(a) of @CIR+10 (proteins differentially abundant at or above 99% confidence level). c. Table 4 of @SRG+10. d. Tables 1 and 2 of @HTP+11. e. f. Supporting Table 6 of @GTM+12. g. Table S1 of @LLL+13. h. i. Table 2 of @SRS+13. For DCIS (3 patients), proteins were classified as up/down regulated if 2 or more ratios were greater/less than 1, and no ratios were less/greater than 1. For IC (4 patients), proteins were classified as up/down regulated if 3 or more ratios were greater/less than 1, and no ratios were less/greater than 1. j. Extracted from Table S2 of @GSB+14. Values in all LFQ columns (distant, near, tumor) were quantile normalized, then the ratio between tumor and distant was calculated. Proteins with normalized LFQ ratios > 1.2 or < 1/1.2 and p-value < 0.05 were identified as differentially expressed. k. Supplementary Tables 12, 13, 14 and 15 of @PPH+14, filtered to include proteins that are up- or down-regulated in all subtypes (LUM, LUMHER, HER, TN). l. Supplemental Data S3 of @CVJ+15, filtered to include proteins with min and max credible intervals for expression ratios that are both <1 or >1. m. n. Supplementary Table S3 of @PGT+16. o. Table S4A of @PBR+16. p. Supplemental Table 4 of @BST+17, filtered to include proteins with p-value < 2. q. r. Tables S5-1 (differentially expressed proteins for 52 tumor / non-cancerous tissue pairs) and S5-2 (13 basal-like tumor / non-cancerous tissue pairs) of @TZD+18, filtered to include proteins with log~2~ fold change > 1 or < -1. s. t. Supplementary File S1 of @GCS+19 (PT: primary breast tissue; NCT: non tumor contralateral breast tissue; ANT: non tumor adjacent breast tissue). u. Supplementary Table 2 of @LLC+19. v. w. Supplementary Tables S2 and S3 of @LLF+20.

References

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