This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins that are differentially expressed in prostate cancer compared to normal tissue. 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% confidence 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 |
GTR+08 (PCa / BPH)
|
35 | 29 | -32 | 4 | -150 | 146 |
| b |
KPB+10 (PCa / adjacent benign)
|
68 | 69 | -17 | 6 | -124 | 129 |
| c |
HZH+12 (PCa / adjacent benign Protein)
|
22 | 37 | -15 | 26 | 50 | -231 |
| d |
JHZ+13 (PCa / adjacent benign)
|
23 | 36 | -22 | 30 | 72 | -84 |
| e |
LCS+14 (glycoproteins PCa / normal)
|
82 | 138 | -8 | 9 | -106 | -6 |
| f |
CZL+16 (protein expression bioinformatics)
|
74 | 157 | -41 | -10 | -56 | 50 |
| g |
IWT+16 (FFPE tumor / adjacent benign)
|
223 | 426 | -27 | 36 | 222 | 116 |
| h |
GLZ+18 (acinar PCa / matched BPH)
|
87 | 114 | -33 | 30 | -59 | 22 |
| i |
GLZ+18 (ductal PCa / matched BPH)
|
347 | 303 | -33 | 10 | -63 | 19 |
| j |
LAJ+18 (PC / BPH)
|
273 | 220 | -35 | 22 | 110 | 86 |
| k |
LAJ+18 (CRPC / BPH)
|
313 | 193 | -25 | 24 | 7 | 19 |
| l |
MAN+18 (PCa / BPH)
|
44 | 33 | 3 | -28 | 36 | -25 |
| m |
KRN+19 (PCa G1 / BPH)
|
32 | 43 | -24 | 28 | 67 | -7 |
| n |
KRN+19 (PCa G2 / BPH)
|
30 | 22 | -39 | 10 | 212 | 226 |
| o |
KRN+19 (PCa G3 / BPH)
|
43 | 24 | -36 | 29 | 189 | 175 |
| p |
KRN+19 (PCa G4 / BPH)
|
44 | 51 | -19 | 20 | 57 | 113 |
| q |
KRN+19 (PCa G5 / BPH)
|
22 | 24 | -15 | 48 | 47 | -35 |
| r |
MMF+20 (FFPE PCa / adjacent benign GS=6)
|
40 | 136 | -16 | -35 | -141 | 11 |
| s |
MMF+20 (FFPE PCa / adjacent benign GS=6 and GS>=8)
|
37 | 143 | -1 | -1 | 18 | -55 |
| t |
TOT+19 (FFPE TMA PCa / normal)
|
36 | 86 | -32 | 34 | -226 | 28 |
| u |
ZYW+19 (OCT LG PCa / adjacent normal)
|
143 | 54 | -43 | 6 | -141 | 116 |
| v |
ZYW+19 (OCT HG PCa / adjacent normal)
|
215 | 94 | -17 | 40 | -208 | 31 |
| w |
KHN+20 (PCa / control)
|
227 | 125 | -19 | 40 | 47 | -85 |
| x |
LDM+20 (PCa / BPH)
|
73 | 72 | -20 | 45 | 2 | -55 |
| y |
SHC+20 (FFPE PCa / BPH)
|
58 | 308 | -34 | 36 | -246 | 52 |
| z |
ZKL+20 (mouse Pten-KO / WT)
|
48 | 55 | 2 | 44 | 49 | -32 |
| A |
ZZX+20 (tumor / normal CiRT)
|
104 | 1451 | -23 | 14 | -241 | 90 |
Gene names or other identifiers were converted to UniProt accession numbers using the UniProt mapping tool.
a. Table 2 of Garbis et al. (2008). b. Supplementary Tables 3 and 4 of Khan et al. (2010). c. Table S2 of Han et al. (2012). d. Table S1 of Jiang et al. (2013). e. Supplemental Table S7 of Liu et al. (2014). f. Supplementary Table 1 Chen et al. (2016) (proteins recorded with only Down-regulation or Up-regulation). g. Supplementary Table S3 of Iglesias-Gato et al. (2016), filtered to include proteins listed with FDR < 0.1. h. i. Extracted from Table S4 Guo et al. (2018). Values were quantile normalized, then ratios were calculated between the median values for each cancer type (acinar and ductal) and corresponding normal tissue; ratios > 1.5 or < 2/3 were used to identify differentially expressed proteins. j. k. Extracted from Supplementary Data 1 of Latonen et al. (2018) (sheet “Area-proteins”) by applying quantile normalization to peak areas then calculating median values across all runs and samples for each of BPH , PC (primary prostate cancer), and CRPC (castration resistant prostate cancer). A cutoff of 2-fold in ratios of medians (PC / BPH or CRPC / BPH) was used to identify differentially expressed proteins. l. Table 2 of Martiny et al. (2018). m. n. o. p. q. Supporting Information Table S3 of Kawahara et al. (2019) (G1–G5: PCa grades). r. s. Tables S4d (GS = 6) and S4f (GS ≥ 8 or GS = 6) of Mantsiou et al. (2020) (GS: Gleason Score). t. Supplementary Table S3a of Turiák et al. (2019). u. v. Table S5 of Zhou et al. (2019) (LG: low-grade PCa; HG: high-grade PCa). w. Supplemental Table S2 of Kwon et al. (2020), filtered to include proteins with log2 fold change > 1 or < -1 in at least one experiment. x. Table S2 of Latosinska et al. (2020). y. Table S2, Sheet D:S3-SWATH_protein_matrix of Sun et al. (2020), filtered to include proteins quantified in at least 50% of both tumor and normal samples and with median fold change > 2 or < 0.5. z. Table S4 of Zhang et al. (2020) (Pten gene knockout vs wild-type). A. Supplementary Tables S3E–S3F of Zhu et al. (2020).
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