This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins associated with transcripts that are differentially expressed in cancer compared to normal tissue (data from The Cancer Genome Atlas and Genotype-Tissue Expression Project via GEPIA2). 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 |
GEPIA2 (ACC)
|
2013 | 391 | -9 | 14 | -207 | 4 |
| b |
GEPIA2 (BLCA)
|
1722 | 735 | -18 | 27 | -114 | 17 |
| c |
GEPIA2 (BRCA)
|
1749 | 1256 | -15 | 13 | -89 | 34 |
| d |
GEPIA2 (CESC)
|
2972 | 1627 | -21 | 17 | -159 | 23 |
| e |
GEPIA2 (COAD)
|
2165 | 2327 | -21 | 12 | -108 | 30 |
| f |
GEPIA2 (DLBC)
|
771 | 7887 | 5 | 15 | -6 | 92 |
| g |
GEPIA2 (ESCA)
|
1088 | 2401 | -1 | 9 | 100 | 64 |
| h |
GEPIA2 (GBM)
|
1883 | 4642 | -12 | -6 | -107 | 89 |
| i |
GEPIA2 (HNSC)
|
557 | 1385 | 3 | -3 | 44 | 30 |
| j |
GEPIA2 (KICH)
|
3002 | 615 | -8 | 0 | -9 | -4 |
| k |
GEPIA2 (KIRC)
|
1141 | 1433 | 5 | 3 | -43 | -8 |
| l |
GEPIA2 (KIRP)
|
1258 | 827 | -3 | 1 | -52 | 35 |
| m |
GEPIA2 (LAML)
|
2578 | 2490 | 9 | -17 | 174 | 12 |
| n |
GEPIA2 (LGG)
|
1376 | 3500 | -6 | -2 | -14 | 79 |
| o |
GEPIA2 (LIHC)
|
570 | 1342 | -4 | 19 | -116 | 76 |
| p |
GEPIA2 (LUAD)
|
2430 | 949 | -14 | 5 | -162 | -19 |
| q |
GEPIA2 (LUSC)
|
3167 | 1654 | -12 | 9 | -143 | 13 |
| r |
GEPIA2 (OV)
|
3567 | 2241 | -15 | 5 | -205 | -56 |
| s |
GEPIA2 (PAAD)
|
335 | 8167 | 4 | 14 | -26 | 79 |
| t |
GEPIA2 (PRAD)
|
1778 | 518 | -34 | 5 | -134 | 52 |
| u |
GEPIA2 (READ)
|
2331 | 2455 | -22 | 11 | -109 | 42 |
| v |
GEPIA2 (SKCM)
|
3007 | 2252 | -16 | 7 | -102 | 41 |
| w |
GEPIA2 (STAD)
|
708 | 3458 | -2 | 8 | -4 | 63 |
| x |
GEPIA2 (TGCT)
|
6227 | 2174 | -12 | 1 | -127 | -23 |
| y |
GEPIA2 (THCA)
|
2341 | 524 | -16 | 6 | -182 | -30 |
| z |
GEPIA2 (THYM)
|
783 | 10099 | 9 | 15 | 44 | 71 |
| A |
GEPIA2 (UCEC)
|
3834 | 1733 | -18 | 12 | -214 | -24 |
| B |
GEPIA2 (UCS)
|
3418 | 1592 | -13 | 14 | -212 | -27 |
a. – B. GEPIA2 (Tang et al., 2019).
Tang Z, Kang B, Li C, Chen T, Zhang Z. 2019. GEPIA2: An enhanced web server for large-scale expression profiling and interactive analysis. Nucleic Acids Research 47:W556–W560. DOI: 10.1093/nar/gkz430.