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 lung 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_lung(2020)

pdat1 <- lapply(datasets, pdat_lung)
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; NSCLC – non-small cell lung cancer; SCC – squamous cell carcinoma; ADC – adenocarcinoma; ANT – adjacent or patient-matched normal (non-malignant, benign) tissue; NBE – normal bronchial epithelium; LCM – laser capture microdissection; FFPE – formalin-fixed paraffin-embedded.
• 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("lung.csv")
write.csv(out, file, row.names = FALSE, quote = 2)

Data Sources

Where given, 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 of @LXC+06. b. c. Gene names from Tables II and III of @KHA+12. d. Gene names from Table 2 of @YLL+12. e. IPI numbers from Table 1 of @ZZD+12. f. Table 2 of @ZZY+13. g. Table 1 of @LLY+14. h. Supplementary data 1b of @LWT+14. i. Supplementary Data of @ZLH+14. j. Gene names from Supporting Information Table S5 of @ZLS+14 (differential expression between normal endothelial cells and both paratumor and tumor endothelial cells). k. Table S3 of @KNT+15 (LPIA: lepidic predominant invasive adenocarcinoma vs pN: pseudo-normal), filtered to include proteins with log~2~ fold change > 1 or < -1 and p-value < 0.05. l. UniProt names from Table S2 of @BLL+16, filtered to include proteins with log~2~ fold change > 1.5 or < -1/1.5 and p-value < 0.05. m. Gene names from Table S2 of @FGP+16. n. Gene names from Table 1 of @JCP+16. o. p. q. Supplemental Table S3B of @HHH+16 (primary tumor / normal comparison; pN0: no nodes involved; pN1: ipsilateral peribronchial/interlobar/hilar LN metastasis; pN2: ipsilateral mediastinal LN metastasis; M1: distant metastasis or malignant effusion). r. Supplemental Table 2 of @TLB+16, filtered with adjusted p-value < 0.05 and fold change ≥ 1.5 or ≤ 2/3. s. Gene names from Supplementary Table S1 of @FGW+17, filtered with p-value < 0.05. t. Table 1 of @LZW+17. u. Supplementary Table S2 of @SFS+17 (sheet LF: label-free quantification). v. Supplementary Table 1 of @WLC+17. w. x. y. z. A. B. Gene names from Tables S2--S6 of @YCC+17 filtered to keep proteins with fold change ≥1.5 or ≤2/3 (Oncogene: oncogene-coded proteins; TSG: tumor suppressor gene-coded proteins; Glycoprotein: glycoproteomics data). C. D. Supplemental Table S2 of @KPS+20 for early (stage I-II) and advanced (stage III-IV) adenocarcinomas. E. Gene names from Table S4D and UniProt IDs from Table S4A of @XZW+20.

References

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