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 colorectal 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_colorectal(2020)

pdat1 <- lapply(datasets, pdat_colorectal)
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; MSS – microsatellite stable; CIS – carcinoma in situ; ICC – invasive colonic carcinoma.
• 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("colorectal.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, except for IPI accession numbers, which were converted using the DAVID 6.7 conversion tool.

a. Table 1 and Supplementary Data 1 of @WTK+08 (Swiss-Prot and UniProt accession numbers from Supplementary Data 2). b. c. IPI accession numbers from Supplemental Table 4 of @XZC+10. d. IPI accession numbers from Supplemental Table 4 of @ZYS+10. e. f. g. h. Gene names from supplemental Table 9 of @BPV+11. i. Supplementary Table 2 of @JCF+11. j. Table S8 of @MRK+11. k. Supplementary Table 1 of @SHHS11. l. Appendix of @FGW+12. m. Gene names from Supplementary Table 4 of @KYK+12, filtered to include proteins with expression ratio > 2 or < 0.5 in both mTRAQ and cICAT analyses. n. Supplementary Table 4 of @WOD+12. o. Table 2 of @CZD+14. p. Ensembl protein IDs from Supporting Table 2 of @STK+15. q. Proteins marked as having a significant change between normal tissue (N) and adenocarcinoma (C) in SI Table 3 of @WDO+15. r. SI Table S3 of @LXM+16, filtered to include proteins with p-value < 0.05. s. t. Gene names from Supplementary Table 4 of @PHL+16, for differential expression between normal colonic mucosa (NC) and carcinoma in situ (CIS) or invasive colorectal cancer (ICC). u. Table S3 of @CTW+17. v. Dataset 6A of @HZW+17. w. Supplementary Material Table S1 of @LLL+17. x. Table 2 of @NKG+17. y. Table S2 of @QMB+17, filtered to include comparisons between adenocarcinoma and diverticular disease. z. Table S1 of @TMS+17, filtered to include proteins that are consistently up- or down-regulated in at least 11 of 12 patients. A. IPI accession numbers from Table S2 of @ZLY+17. B. Supplementary Table 1B of @AKG+18, filtered to include proteins with expression ratio > 3/2 or < 2/3. C. D. Supplementary Table S2 of @STA+19, filtered to include proteins with log~2~ ratio > ± the standard deviation of values for all quantified proteins. E. Online data from @VHW+19 (file: HumanCPTAC_COADPNNLProteomeTMT03_01_2017BCMGeneTumor_Normal_log2FC.cct), filtered to include proteins with median log~2~ ratio > 1 or < -1. F. Supplementary Information Table S2 of @WYL+19.

References

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