This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins that are differentially expressed in hypoxia compared to control conditions. 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 |
SBB+06 (mouse malignant melanoma plasma membrane)
|
574 | 289 | -2 | 10 | 112 | -50 |
| b |
FWH+13 (THP-1 macrophages)
|
56 | 40 | 8 | 14 | 18 | -92 |
| c |
RHD+13 (A431 epithelial carcinoma cells Hx48)
|
211 | 92 | 9 | -1 | 78 | -73 |
| d |
RHD+13 (A431 epithelial carcinoma cells Hx72)
|
88 | 67 | -19 | -21 | 72 | -86 |
| e |
VTMF13 (SH-SY5Y neuroblastoma cells)
|
141 | 64 | -13 | 31 | -4 | 1 |
| f |
DCH+14 (mouse 4T1 cells)
|
71 | 60 | 16 | -33 | -300 | 7 |
| g |
DYL+14 (A431 epithelial carcinoma cells Hx48-S)
|
65 | 34 | 30 | -45 | 122 | -51 |
| h |
DYL+14 (A431 epithelial carcinoma cells Hx72-S)
|
137 | 61 | 2 | -28 | 18 | -50 |
| i |
DYL+14 (A431 epithelial carcinoma cells Hx48-P)
|
74 | 44 | 7 | -6 | 124 | 113 |
| j |
DYL+14 (A431 epithelial carcinoma cells Hx72-P)
|
67 | 53 | -9 | -13 | 20 | 2 |
| k |
BSA+15 (HeLa cervical cancer cells)
|
53 | 72 | 6 | -17 | 225 | -155 |
| l |
HWA+16 (U87MG and 786-O cancer cells)
|
137 | 164 | 0 | -23 | 22 | -75 |
| m |
LCS16 (HCT116 colon cancer translation)
|
469 | 1024 | -21 | -21 | 323 | 38 |
| n |
CGH+17 (mouse cardiac fibroblasts whole)
|
38 | 48 | -12 | 16 | -374 | 33 |
| o |
ZXS+17 (U87 and U251 glioblastoma cells)
|
143 | 122 | 26 | -57 | 61 | 3 |
| p |
CLY+18 (HCT116 colon cancer cells proteome)
|
108 | 127 | -6 | 8 | -117 | -159 |
| q |
GBH+18 (SW620 colorectal cancer cells)
|
237 | 67 | 9 | -4 | -12 | -1 |
| r |
LKK+18 (hUCB mesehnchymal stem cells)
|
44 | 62 | 8 | 38 | 65 | 73 |
| s |
WTG+18 (adipose-derived mesehnchymal stem cells)
|
163 | 57 | 9 | -32 | 49 | 10 |
| t |
CSK+19 (HeLa cervical cancer cells)
|
36 | 45 | 4 | 1 | 6 | -47 |
| u |
GPT+19 (MIAPaCa-2 pancreatic cancer cells pulse/trace Light serum replete)
|
62 | 180 | 2 | 19 | -44 | -43 |
| v |
GPT+19 (MIAPaCa-2 pancreatic cancer cells pulse/trace Heavy serum replete)
|
196 | 57 | -10 | 7 | -160 | -106 |
| w |
KAN+19 (cancer-associated fibroblasts proteome)
|
221 | 124 | 20 | -4 | 114 | 86 |
| x |
LLL+19 (human periodontal ligament cells)
|
67 | 153 | -27 | 32 | -216 | -9 |
| y |
BCMS20 (MCF-7 breast cancer cells)
|
153 | 161 | 19 | -38 | -192 | -108 |
| z |
RVN+20 (PC-3 prostate cancer cells in DMSO)
|
116 | 86 | -40 | -20 | 230 | 32 |
| A |
RVN+20 (PC-3 prostate cancer cells in NO.sul)
|
28 | 33 | -15 | -7 | 247 | 82 |
| B |
RVN+20 (PC-3 prostate cancer cells in sul)
|
17 | 54 | -47 | -11 | -203 | 34 |
| C |
RVN+20 (PC-3 prostate cancer cells in DMSO.4Gy)
|
24 | 38 | -20 | -21 | 40 | -119 |
| D |
RVN+20 (PC-3 prostate cancer cells in NO.sul.4Gy)
|
21 | 52 | 46 | -4 | 88 | 82 |
| E |
RVN+20 (PC-3 prostate cancer cells in sul.4Gy)
|
34 | 25 | 15 | -46 | -54 | -110 |
| F |
SPJ+20 (canine POS cells)
|
43 | 102 | 4 | -22 | -30 | 7 |
| G |
SPJ+20 (canine HMPOS cells)
|
62 | 69 | 5 | -15 | -74 | -8 |
Where given, gene names or other identifiers were converted to UniProt accession numbers using the UniProt mapping tool.
a. Supplemental Table 1 of Stockwin et al. (2006), filtered to include proteins with expression ratio ≥ 1.7 or ≤ 0.58. b. Supplemental Table 2A of Fuhrmann et al. (2013) (control virus cells). c. d. Supplemental Table S1 of Ren et al. (2013), filtered to include proteins with iTRAQ ratios < 0.83 or > 1.2 and p-value < 0.05. e. Supporting Information table of Villeneuve et al. (2013), filtered to include proteins with a normalized expression ratio of > 1.2 or < 0.83. f. Supporting Information Table S1 Djidja et al. (2014). g. h. i. j. Supplemental Table S1 of Dutta et al. (2014), filtered to include proteins with p-value < 0.05 (-S: supernatant fraction; -P: pellet fraction). k. Supplementary Table S1 of Bousquet et al. (2015). l. Supplemental Information Table S1 of Ho et al. (2016), filtered to include proteins with a fold change of < 0.5 or > 1 and that were detected in only hypoxic or only normoxic conditions. m. Gene names from Lai, Chang & Sun (2016) (data files provided by Ming-Chih Lai). n. Extracted from Table S2E (whole cell lysate) of Cosme et al. (2017), keeping proteins with FDR < 0.05. o. Supplemental Table S4 of Zhang et al. (2017). p. Supplementary Tables S6-S7 (proteome) of Chen et al. (2018). q. List of up- and down-regulated proteins from Greenhough et al. (2018) (provided by Alex Greenhough), filtered to include proteins with average fold change ≥ 1.5 or ≤ 2/3. r. Gene names from Figure 1F of Lee et al. (2018). s. Supplemental file 1 of Wobma et al. (2018) (provided by Gordana Vunjak-Novakovic), filtered to include proteins with Normalized Ratio [Hypoxia MSC/Control MSC] ≥ 1.5 or ≤ 2/3 and p-value < 0.05. t. Gene names from Supplementary file S1 of Chachami et al. (2019) for the two replicates labelled as “input_Log2ratioHL_firstIP” and “input_Log2ratioLH_secondIP” (soluble extracts before immunoprecipitation), filtered to include proteins where Log2ratio is > 0.2 or < -0.2 for both replicates. u. v. Supplementary Data 1 of Gupta et al. (2019), filtered to include proteins with p-value < 0.05 and fold-change > 2 or < 0.5 w. Proteins identified as up- or down-regulated > 1 SD in Data File S1 of Kugeratski et al. (2019) (sheet “Proteome”). x. Additional file 1: Table S1 of Li et al. (2019). y. Gene names from Supplementary Information Tables S6 and S7 of Bush et al. (2020). z. A. B. C. D. E. Supplementary Table 1A of Ross et al. (2020), filtered to include proteins with median fold change between normoxic and hypoxic conditions in any individual treatment > 1.5 or < 2/3. F. G. Supplementary Tables S3b (sheet “HPNP”) and S3c (sheet “HHNH”) of Song et al. (2020).
Thanks to Alex Greenhough, Ming-Chih Lai, and Gordana Vunjak-Novakovic for providing data files.
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