In jedick/JMDplots: Plots from Papers by Jeffrey M. Dick

This vignette from the R package JMDplots version r packageDescription("JMDplots")$Version approximately reproduces calculations of compositional oxidation state and hydration state that are described in a paper published in PeerJ (Dick, 2017). The reproduction is not exact because of data updates made in the package after the paper was published.

Abbreviations

U937 (acute promonocytic leukemic cells), B104 (rat neuroblastoma cells), DU145 (prostate carcinoma cells), SK-N-BE(2)c; IMR-32; SH-SY5Y (neuroblastoma cells), H9C2 (rat heart myoblast), MCF-7 (breast cancer cells), THP-1 (macrophages), A431 (epithelial carcinoma cells), Hx48 (hypoxia 48 h), Hx72 (hypoxia 72 h), ReOx (hypoxia 48 h followed by reoxygenation for 24 h), -S (supernatant fraction), -P (pellet fraction), SPH (spheroids), HepG2/C3A (hepatocellular carcinoma cells), U87MG (glioblastoma), 786-O (renal clear cell carcinoma cells), HCT116; HT29 (colon cancer cells), SC (stem cells), SAL (salidroside).

Summary Table

This table compares the chemical compositions of groups of proteins that are relatively down- and up-expressed (n1 and n2, respectively) in cells grown in hypoxia or 3D culture compared to control conditions.

options(width = 90)

library(canprot)

datasets <- pdat_hypoxia(2017)

pdat <- lapply(datasets, pdat_hypoxia)
comptab <- lapply(pdat, get_comptab, plot.it = FALSE, mfun = "mean", oldstyle = TRUE)

library(xtable)
out <- xsummary(comptab)
# round values and include dataset tags
tags <- sapply(sapply(strsplit(datasets, "="), "[", -1), paste, collapse = ";")
out <- cbind(out[, 1:2], tags = tags, out[, 3:14])
out[, 6:15] <- round(out[, 6:15], 4)
write.csv(out, "hypoxia.csv", row.names = FALSE, quote = 2)

Data Sources

a. 2% O₂ vs normoxic conditions. Source: Table 1 of @HXS+06. b. 1% vs 6% O₂. Source: Tables 2 and 3 of @BRA+10. c. The comparisons here use expression ratios HYP/LSC (oxygen deprivation / low serum control) >1.2 or <0.83, calculated from the reported ratios. Source: extracted from Suppl. Table 2 of @DPL+10, including proteins with p-value <0.05 and EF <1.4. d. Translationally regulated genes. Source: Suppl. Tables 1–4 of @BMJ+11. e. 1% O₂ for 72 h vs standard conditions. Source: Suppl. Table 1(a) of @CBW+11. f. Hypoxic vs control conditions for 16 h. Source: Suppl. Table S5 of @LAR+12. g. h. Tumourspheres (50 to 200 μm diameter) at passage 5 (P5) or 2 (P2) compared to adherent cells. Source: Sheets 2 and 3 in Table S1 of @MHG+12. i. j. Perinecrotic and necrotic regions compared to surface of multicell spheroids (~600 μm diameter). The comparisons here use expression ratios <0.77 or >1.3. Source: Suppl. Table 1C of @MVC+12. k. Incubation for several days under hypoxia (1% O₂). Source: Suppl. Table 2A of @FWH+13 (control virus cells). l. m. n. Source: extracted from Suppl. Table 1 of @RHD+13, including proteins with iTRAQ ratios <0.83 or >1.2 and p-value <0.05. o. 5% O₂ vs atmospheric levels of O₂. The comparisons here include proteins with a normalized expression ratio of >1.2 or <0.83. Source: SI table of @VTMF13. p. q. r. s. t. u. The comparisons here include proteins with p <0.05. Source: Suppl. Table S1 of @DYL+14. v. Organotypic spheroids (~250 μm diameter) vs lysed CRC tissue. Source: extracted from Table S2 of @RKP+14, filtered as follows: at least two of three experiments have differences in spectral counts, absolute overall fold change is at least 1.5, and p-value is less than 0.05. w. SPH vs classical cell culture (2D growth). Standard concentrations of gases used for tissue culture (5% CO₂, 95% air) were used in both cases. The comparisons here include proteins that have a log₂ fold change of at least ±1. Source: P1_Data sheet in the SI of @WRK+14. x. 1% vs 19% O₂. Source: Table S1 of @BSA+15. y. 1% O₂ for 24 hr. The comparisons here include proteins with a fold change of <0.5 or >1 and proteins that were detected in only hypoxic or only normoxic conditions. Source: Table S1 of @HWA+16. z. A. Microarray analysis of differential gene expression in the transcriptome (total rRNA) and translatome (polysomal / total RNA ratio) of cells grown in normal and hypoxic (1% O₂) conditions. Source: data file supplied by Dr. Ming-Chih Lai (@LCS16). B. ASC from 3 donors cultured for 24 hr. in hypoxic (1% O₂) vs normoxic (20% O₂) conditions. Source: Tables 1 and 2 of @RSE+16. C. D. Rat cardiomyocytes treated with CoCl₂ (hypoxia mimetic) vs control or with SAL (anti-hypoxic) vs CoCl₂. Source: SI Tables 1S and 2S of @XCJ+16. E. 800 μm spheroids vs 2D monolayers. Source: Tables S1a–b of @YLW+16.

Mean Differences

The reoxygenation or anti-hypoxic, tumor spheroid, and adipose-derived stem cell datasets are highlighted in blue, red, and orange, respectively.

col <- rep("black", length(datasets))
col[grepl("ReOx", datasets)] <- "blue"
col[grepl("=SPH", datasets)] <- "red"
col[grepl("=ASC", datasets)] <- "orange"
diffplot(comptab, col = col, oldstyle = TRUE)