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

This vignette runs the code to make the plots from the following paper:

Dick JM. 2021. Water as a reactant in the differential expression of proteins in cancer. Computational & Systems Oncology 1(1): e1007. doi: 10.1002/cso2.1007

This vignette was compiled on 2023-02-13 with JMDplots 1.2.17 and canprot 1.1.2-5.

library(JMDplots)
# Read canprot's 'basis' option
basis <- getOption("basis")

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 protein length, nH2O and ZC for cell culture and cancer tissue (Figure 2)

canH2O2()

nH2O-ZC 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")
ΔZC ΔnH2O
hypoxia 0.000 (-0.0) -0.010 (-1.6)
secreted 0.011 (-1.4) -0.002 (-0.1)
salt -0.003 (-0.5) -0.011 (-1.1)
glucose -0.001 (-0.1) -0.015 (-2.4)
3D -0.011 (-2.0) -0.016 (-3.3)
breast -0.012 (-2.7) 0.018 (-2.7)
colorectal 0.005 (-1.1) 0.015 (-3.9)
liver 0.018 (-6.7) 0.014 (-3.7)
lung -0.006 (-1.2) 0.019 (-4.3)
pancreatic 0.013 (-2.2) 0.011 (-1.3)
prostate -0.023 (-9.2) 0.019 (-4.3)
TCGA -0.009 (-4.0) 0.008 (-4.3)
HPA -0.000 (-0.0) 0.010 (-4.0)
up 0.014 (-2.8) -0.009 (-0.7)
down 0.003 (-0.3) -0.016 (-2.1)

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

canH2OS1()

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

canH2OS2()