This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins that are differentially expressed in colorectal 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 |
WTK+08 (T / N)
|
57 | 70 | 1 | 2 | -64 | 5 |
| b |
XZC+10 (stage I / normal)
|
48 | 166 | -3 | 10 | -100 | -16 |
| c |
XZC+10 (stage II / normal)
|
77 | 321 | 11 | 2 | 4 | -21 |
| d |
ZYS+10 (microdissected T / N)
|
60 | 57 | 18 | 18 | -7 | -38 |
| e |
BPV+11 (stage I / normal)
|
109 | 72 | 3 | -12 | 42 | -101 |
| f |
BPV+11 (stage II / normal)
|
164 | 140 | 19 | 0 | 93 | -29 |
| g |
BPV+11 (stage III / normal)
|
63 | 131 | 23 | -13 | -36 | 38 |
| h |
BPV+11 (stage IV / normal)
|
42 | 26 | -8 | 16 | -28 | -110 |
| i |
JCF+11 (T / N)
|
72 | 45 | 16 | -2 | -36 | -20 |
| j |
MRK+11 (adenocarcinoma / normal)
|
350 | 232 | 28 | 36 | 212 | 35 |
| k |
SHHS11 (LCM T / N)
|
28 | 43 | -16 | 21 | 62 | -114 |
| l |
FGW+12 (T / matched N)
|
48 | 34 | -22 | 50 | 48 | 156 |
| m |
KYK+12 (MSS-type T / N)
|
73 | 175 | 20 | 6 | 125 | 70 |
| n |
WOD+12 (LCM FFPE T / adjacent N)
|
79 | 677 | 9 | 27 | 193 | 157 |
| o |
CZD+14 (T / N)
|
52 | 74 | 6 | 43 | -160 | 51 |
| p |
STK+15 (membrane enriched T / N)
|
113 | 66 | -4 | 7 | 6 | 100 |
| q |
WDO+15 (LCM FFPE T / adjacent N)
|
879 | 1281 | 14 | 25 | 129 | 44 |
| r |
LXM+16 (biopsy T / N)
|
191 | 178 | -4 | 15 | -24 | 65 |
| s |
PHL+16 (CIS / N)
|
169 | 138 | 16 | -6 | 284 | 142 |
| t |
PHL+16 (ICC / N)
|
129 | 100 | 19 | -20 | 309 | 160 |
| u |
CTW+17 (organoid T / N)
|
227 | 78 | -2 | 24 | -120 | 66 |
| v |
HZW+17 (T / adjacent N)
|
126 | 589 | 11 | 24 | 172 | 130 |
| w |
LLL+17 (LCM cancer / non-neoplastic mucosa)
|
110 | 77 | -6 | 10 | 247 | 148 |
| x |
NKG+17 (T / N)
|
48 | 77 | 10 | -15 | -68 | -66 |
| y |
QMB+17 (FFPE T / N)
|
25 | 53 | -23 | 53 | -63 | 4 |
| z |
TMS+17 (epithelial T / N)
|
158 | 166 | 29 | 17 | 61 | 70 |
| A |
ZLY+17 (T / N)
|
58 | 54 | 18 | 13 | -22 | -11 |
| B |
AKG+18 (T / N)
|
43 | 426 | -31 | 32 | -46 | 56 |
| C |
STA+19 (non-metastatic colon cancer, T / N)
|
437 | 317 | 11 | 30 | 78 | 57 |
| D |
STA+19 (metastatic colon cancer, T / N)
|
436 | 356 | 25 | 40 | 68 | 9 |
| E |
VHW+19 (T / adjacent N)
|
417 | 31 | -32 | 33 | -49 | 106 |
| F |
WYL+19 (tumor-associated / normal vascular endothelial cells)
|
97 | 119 | 10 | -15 | -150 | 162 |
Gene names or other identifiers were converted to UniProt accession numbers using the UniProt mapping tool, except for IPI accession numbers, which were converted using the DAVID 6.7 conversion tool.
a. Table 1 and Supplementary Data 1 of Watanabe et al. (2008) (Swiss-Prot and UniProt accession numbers from Supplementary Data 2). b. c. IPI accession numbers from Supplemental Table 4 of Xie et al. (2010). d. IPI accession numbers from Supplemental Table 4 of Zhang et al. (2010). e. f. g. h. Gene names from supplemental Table 9 of Besson et al. (2011). i. Supplementary Table 2 of Jankova et al. (2011). j. Table S8 of Mikula et al. (2011). k. Supplementary Table 1 of Shi et al. (2011). l. Appendix of Fan et al. (2012). m. Gene names from Supplementary Table 4 of Kang et al. (2012), filtered to include proteins with expression ratio > 2 or < 0.5 in both mTRAQ and cICAT analyses. n. Supplementary Table 4 of Wiśniewski et al. (2012). o. Table 2 of Chen et al. (2014). p. Ensembl protein IDs from Supporting Table 2 of Sethi et al. (2015). q. Proteins marked as having a significant change between normal tissue (N) and adenocarcinoma (C) in SI Table 3 of Wiśniewski et al. (2015). r. SI Table S3 of Liu et al. (2016), filtered to include proteins with p-value < 0.05. s. t. Gene names from Supplementary Table 4 of Peng et al. (2016), for differential expression between normal colonic mucosa (NC) and carcinoma in situ (CIS) or invasive colorectal cancer (ICC). u. Table S3 of Cristobal et al. (2017). v. Dataset 6A of Hao et al. (2017). w. Supplementary Material Table S1 of Li et al. (2017). x. Table 2 of Nishio et al. (2017). y. Table S2 of Quesada-Calvo et al. (2017), filtered to include comparisons between adenocarcinoma and diverticular disease. z. Table S1 of Tu et al. (2017), filtered to include proteins that are consistently up- or down-regulated in at least 11 of 12 patients. A. IPI accession numbers from Table S2 of Zhang et al. (2017). B. Supplementary Table 1B of Atak et al. (2018), filtered to include proteins with expression ratio > 3/2 or < 2/3. C. D. Supplementary Table S2 of Saleem et al. (2019), filtered to include proteins with log2 ratio > ± the standard deviation of values for all quantified proteins. E. Online data from Vasaikar et al. (2019) (file: Human__CPTAC_COAD__PNNL__Proteome__TMT__03_01_2017__BCM__Gene__Tumor_Normal_log2FC.cct), filtered to include proteins with median log2 ratio > 1 or < -1. F. Supplementary Information Table S2 of Wang et al. (2019).
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