This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins that are differentially expressed in cancer compared to normal tissue (data from The Human Protein Atlas). The analysis is described in more detail in a paper (Dick, 2021). Abbreviations:
Differences are calculated as (median value for up-regulated proteins) - (median value for down-regulated proteins). Dashed lines enclose the 50% credible region for highest probability density.
In the table, values of ΔZC and ΔnH2O are multiplied by 1000, values of ΔMW are multiplied by 100, and negative values are shown in bold. Abbreviations:
| set | reference (description) | ndown | nup | ΔZC | ΔnH2O | ΔnAA | ΔMW |
|---|---|---|---|---|---|---|---|
| a |
HPA19 (breast cancer / breast)
|
77 | 512 | -4 | 21 | -9 | -14 |
| b |
HPA19 (cervical cancer / cervix, uterine)
|
367 | 207 | -3 | 4 | 52 | -52 |
| c |
HPA19 (colorectal cancer / colon)
|
263 | 423 | -6 | 4 | 48 | -41 |
| d |
HPA19 (endometrial cancer / endometrium 1)
|
117 | 263 | -22 | 1 | -33 | 68 |
| e |
HPA19 (glioma / cerebral cortex)
|
95 | 209 | -1 | 9 | 25 | -3 |
| f |
HPA19 (head and neck cancer / salivary gland)
|
1075 | 534 | 12 | 10 | 96 | 16 |
| g |
HPA19 (liver cancer / liver)
|
51 | 423 | 6 | 6 | -39 | 5 |
| h |
HPA19 (lung cancer / lung)
|
402 | 268 | -3 | 15 | -14 | 5 |
| i |
HPA19 (lymphoma / lymph node)
|
446 | 69 | 0 | 13 | 42 | -20 |
| j |
HPA19 (melanoma / skin 1)
|
180 | 516 | -5 | -3 | -36 | -33 |
| k |
HPA19 (ovarian cancer / ovary)
|
151 | 1075 | -9 | 19 | -21 | -3 |
| l |
HPA19 (pancreatic cancer / pancreas)
|
361 | 293 | 8 | 7 | 39 | 7 |
| m |
HPA19 (prostate cancer / prostate)
|
621 | 197 | 5 | -9 | -14 | 10 |
| n |
HPA19 (renal cancer / kidney)
|
939 | 97 | -12 | 7 | -35 | -44 |
| o |
HPA19 (stomach cancer / stomach 1)
|
1963 | 111 | 20 | 12 | 33 | -34 |
| p |
HPA19 (testis cancer / testis)
|
1202 | 123 | 10 | 19 | 70 | -78 |
| q |
HPA19 (thyroid cancer / thyroid gland)
|
784 | 387 | -11 | 2 | -15 | -17 |
| r |
HPA19 (urothelial cancer / urinary bladder)
|
1050 | 94 | 13 | 17 | 35 | -36 |
a. – r. Human Protein Atlas (Uhlén et al., 2015).
Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, Mardinoglu A, Sivertsson Å, Kampf C, Sjöstedt E, Asplund A, Olsson I, Edlund K, Lundberg E, Navani S, Szigyarto CA-K, Odeberg J, Djureinovic D, Takanen JO, Hober S, Alm T, Edqvist P-H, Berling H, Tegel H, Mulder J, Rockberg J, Nilsson P, Schwenk JM, Hamsten M, Feilitzen K von, Forsberg M, Persson L, Johansson F, Zwahlen M, Heijne G von, Nielsen J, Pontén F. 2015. Tissue-based map of the human proteome. Science 347:1260419. DOI: 10.1126/science.1260419.