This vignette was compiled on 2025-05-20 with JMDplots 1.2.22 and canprot 2.0.0.

The QEC basis species (glutamine, glutamic acid, cysteine, H₂O, O₂) are used for the analysis of stoichiometric hydration state (nH₂O).

Study overview (Figure 1)

canH2O1()

Median differences of nH₂O and Z_C for cell culture and cancer tissue (Figure 2)

canH2O2()

nH₂O-Z_C plots for TCGA and HPA datasets (Figure 3)

canH2O3()

Differentially expressed genes in aneuploid and osmotically shocked yeast cells (Figure 4)

canH2O4()

Mean differences and p-values for all datasets in each condition (Table 2)

Mean differences are followed by log₁₀ of p-value in parentheses. Mean differences are computed as (mean of median values for up-regulated proteins in each dataset) - (mean of median values for down-regulated proteins in each dataset). The rows labelled “up” and “down” refer to (mean of median values for [up- or down-]regulated proteins in secreted proteins in hypoxia) - (mean of median values for [up-or down-]regulated proteins in whole-cell extracts in hypoxia).

kable(canH2OT2(), align = "r")

	ΔZ_C	Δn_H2O
hypoxia	0.000 (-0.0)	-0.009 (-1.6)
secreted	0.011 (-1.4)	-0.003 (-0.1)
salt	-0.003 (-0.5)	-0.010 (-1.0)
glucose	-0.001 (-0.1)	-0.014 (-2.4)
3D	-0.011 (-2.0)	-0.017 (-3.4)
breast	-0.012 (-2.7)	0.018 (-2.6)
colorectal	0.005 (-1.1)	0.015 (-3.8)
liver	0.018 (-6.7)	0.015 (-4.0)
lung	-0.006 (-1.2)	0.019 (-4.1)
pancreatic	0.013 (-2.2)	0.012 (-1.5)
prostate	-0.023 (-9.2)	0.019 (-4.1)
TCGA	-0.009 (-4.0)	0.008 (-4.0)
HPA	-0.000 (-0.0)	0.009 (-3.6)
up	0.014 (-2.8)	-0.008 (-0.7)
down	0.003 (-0.3)	-0.015 (-1.9)

Supplementary Tables and Figures

Stoichiometric matrix for amino acids with QEC basis species (Table S1)

kable(canH2OT1())

	C₅H₁₀N₂O₃	C₅H₉NO₄	C₃H₇NO₂S	H₂O	O₂
alanine	0.4	0.2	0	0.6	-0.3
cysteine	0.0	0.0	1	0.0	0.0
aspartic acid	0.2	0.6	0	-0.2	0.6
glutamic acid	0.0	1.0	0	0.0	0.0
phenylalanine	-0.8	2.6	0	-2.2	-1.9
glycine	0.6	-0.2	0	0.4	0.3
histidine	1.8	-0.6	0	-1.8	0.4
isoleucine	-0.2	1.4	0	1.2	-2.1
lysine	0.8	0.4	0	1.2	-1.6
leucine	-0.2	1.4	0	1.2	-2.1
methionine	-0.4	0.8	1	0.4	-1.2
asparagine	1.2	-0.4	0	-0.2	0.6
proline	0.0	1.0	0	0.0	-1.0
glutamine	1.0	0.0	0	0.0	0.0
arginine	2.8	-1.6	0	0.2	-0.1
serine	0.4	0.2	0	0.6	0.2
threonine	0.2	0.6	0	0.8	-0.4
valine	0.0	1.0	0	1.0	-1.5
tryptophan	-0.2	2.4	0	-3.8	-1.6
tyrosine	-0.8	2.6	0	-2.2	-1.4

nO₂-Z_C and nH₂O-Z_C correlations using QEC basis species (Figure S1)

canH2OS1()

HPA-TCGA scatterplots for Z_C and nH₂O (Figure S2)

canH2OS2()

JMDplots vignettes

Water as a reactant in the differential expression of proteins in cancer (2021)

Study overview (Figure 1)

Median differences of nH₂O and Z_C for cell culture and cancer tissue (Figure 2)

nH₂O-Z_C plots for TCGA and HPA datasets (Figure 3)

Differentially expressed genes in aneuploid and osmotically shocked yeast cells (Figure 4)

Mean differences and p-values for all datasets in each condition (Table 2)

Supplementary Tables and Figures

Stoichiometric matrix for amino acids with QEC basis species (Table S1)

nO₂-Z_C and nH₂O-Z_C correlations using QEC basis species (Figure S1)

HPA-TCGA scatterplots for Z_C and nH₂O (Figure S2)

JMDplots vignettes

Water as a reactant in the differential expression of proteins in cancer (2021)

Study overview (Figure 1)

Median differences of nH2O and ZC for cell culture and cancer tissue (Figure 2)

nH2O-ZC plots for TCGA and HPA datasets (Figure 3)

Differentially expressed genes in aneuploid and osmotically shocked yeast cells (Figure 4)

Mean differences and p-values for all datasets in each condition (Table 2)

Supplementary Tables and Figures

Stoichiometric matrix for amino acids with QEC basis species (Table S1)

nO2-ZC and nH2O-ZC correlations using QEC basis species (Figure S1)

HPA-TCGA scatterplots for ZC and nH2O (Figure S2)

Median differences of nH₂O and Z_C for cell culture and cancer tissue (Figure 2)

nH₂O-Z_C plots for TCGA and HPA datasets (Figure 3)

nO₂-Z_C and nH₂O-Z_C correlations using QEC basis species (Figure S1)

HPA-TCGA scatterplots for Z_C and nH₂O (Figure S2)