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 liver 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_liver(2020)

pdat1 <- lapply(datasets, pdat_liver)
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; EGF – epidermal growth factor; G1, G2, G3 – well-differentiated, moderately differentiated, poorly differentiated tumors; T1, T2, T3 – T1N0M0, T2N0M0, T3N0M0 tumor-node-metastasis classification.
• 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("liver.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 III of @LHT+04. b. Tables 2 and 3 of @BLP+05. c. Table 2 of @LTZ+05. d. Table 1 of @DTS+07, including proteins identified in either tumor homogenates or laser microdissected samples. e. Supplemental Table S1 of @SXS+07. f. Tables 1--3 of @CHN+08. g. Supplemental Tables S3A and S3C of @RLA+10, filtered to include proteins with p-value < 0.05. h. i. IPI numbers from Supplemental Tables S3 (nuclear proteins) and S4 (cytoskeletal proteins) of @LMG+11, filtered to include proteins with median fold-change > 2 or < 0.5. j. Supplemental Table 5 of @LRL+12. k. Supplementary Table 3 of @KOK+13. l. Supplemental Data S5 (sheet "LF_proteins") of @MBK+13. m. Supporting Information SI-S2 of @XWS+14. n. Table 1 of @BSG15. o. Supplementary Table S1 of @RPM+15, filtered to include proteins with > 1 peptide used for quantification and fold change > 2 in either direction. p. q. r. Supplementary Data Table S2 of @NBM+16 (sheets "G1 vs C", "G2 vs C", and "G3 vs C"), filtered to include proteins with p-value < 0.05, quantified in at least half of both tumor and control samples, and median log~2~ fold change > 1 or < -1. s. Supporting Information Table S-4 (sheet "Filtered protein list") of @NMB+16. t. u. v. Supplementary Tables S3--S5 of @QXC+16. w. Table 4 of @GJZ+17. x. Supplementary Table S5 of @GWS+17. y. Supplementary Table 5 of @QPP+17, filtered to include proteins with median fold change > 2 or < 0.5 (UniProt IDs from Supplementary Table 1). z. A. B. C. Supplementary Table S3 of @WLL+17, filtered to include proteins with p-value < 0.05 and fold change > 2 or < 0.5. D. Supplemental Table S2 of @BOK+18 (data for tumor vs. peritumor), filtered to include proteins with q-value < 0.05, quantified in at least 3 tumors, same direction of change in all tumors, and median log~2~ fold change > 1 or < -1. E. Supplementary Table S2 of @YXZ+18. F. Dataset of @BEM+20, filtered to include proteins quantified in more than half of each of control and cancer samples and median fold change > 2 or < 0.5. G. H. Supplemental Table S3 of @GZD+19 (sheets "1. 1,274 DF proteins" and "2. 859 DF phosphoproteins"), filtered to include proteins with log~2~ fold change > 1 or < -1. I. Supplementary Table 6 of @JSZ+19. J. Supporting Information Table S5 of @ZZL+19 (sheet "c_proteins"), filtered to include proteins quantified in at least half of tumor and normal samples and with fold change > 2 or < 0.5. K. Supporting Information Table S4 of @GZL+20 (sheet "B_Molecule"). L. M. Supplementary Tables S1--S2 (proteins with differential expression between non-tumor and tumor regions) and S3--S4 (all proteins identified in each region) of @SCL+20. Common accession numbers in Tables S3 and S4 were eliminated to yield proteins uniquely identified in either tumor or non-tumor regions.

References

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