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 2024-03-23 with JMDplots 1.2.19-13 and canprot 1.1.2-42.
The QEC basis species (glutamine, glutamic acid, cysteine, H2O, O2) are used for the analysis of stoichiometric hydration state (nH2O).
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).
ΔZC | ΔnH2O | |
---|---|---|
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) |
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 |