This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins that are differentially expressed in 3D compared to 2D culture 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 |
PLC+10 (HepG2 hepatocellular carcinoma cells)
|
35 | 47 | -4 | 34 | -155 | 165 |
| b |
MHG+12 (MCF-7 breast cancer cells P5)
|
409 | 337 | -18 | -10 | -194 | -33 |
| c |
MHG+12 (MCF-7 breast cancer cells P2)
|
248 | 214 | -14 | -3 | -168 | -69 |
| d |
MVC+12 (HT29 colon cancer cells perinecrotic)
|
48 | 52 | -5 | -13 | 128 | -11 |
| e |
MVC+12 (HT29 colon cancer cells necrotic)
|
101 | 186 | -20 | -21 | 118 | -29 |
| f |
YYW+13 (HNSCC tumor spheres)
|
58 | 65 | 0 | -9 | 44 | -107 |
| g |
ZMH+13 (HUVEC Matrigel 12h)
|
48 | 58 | -15 | -14 | 180 | -141 |
| h |
ZMH+13 (HUVEC Matrigel 24h)
|
196 | 239 | -26 | -42 | 143 | -95 |
| i |
HKX+14 (U251 glioma cells)
|
295 | 68 | 4 | -27 | 121 | -113 |
| j |
KDS+14 (hESC spheroids)
|
270 | 52 | -9 | -18 | 52 | 62 |
| k |
KDS+14 (hiPSC spheroids)
|
422 | 53 | -8 | -13 | 16 | 88 |
| l |
KDS+14 (hPSC spheroids)
|
612 | 98 | -11 | -27 | -32 | 22 |
| m |
RKP+14 (colorectal cancer-derived cells)
|
93 | 174 | 15 | 3 | -82 | 75 |
| n |
SAS+14 (SK-N-BE2 neuroblastoma spheroids)
|
70 | 116 | 10 | -17 | -117 | 14 |
| o |
WRK+14 (HepG2/C3A hepatocellular carcinoma)
|
125 | 291 | -22 | -24 | 22 | 116 |
| p |
MTK+15 (OV-90AD ovarian cancer multicellular aggregates)
|
39 | 90 | -15 | -40 | -30 | -74 |
| q |
YLW+16 (HT29 colon carcinoma)
|
116 | 225 | -36 | -19 | -108 | -39 |
| r |
KJK+18 (SW480 colorectal cancer)
|
247 | 136 | -56 | -34 | 98 | -2 |
| s |
TGD18 (normal human skin fibroblasts)
|
15 | 57 | 28 | -33 | -185 | 142 |
| t |
TGD18 (cancer-associated fibroblasts)
|
43 | 90 | 27 | -37 | 30 | 28 |
| u |
EWK+19 (glioblastoma spheroids)
|
110 | 171 | 4 | 16 | 86 | -72 |
| v |
GADS19 (skin fibroblasts)
|
94 | 49 | 11 | -34 | 196 | 134 |
| w |
HLC19 (HepG2 hepatocellular carcinoma cells)
|
573 | 590 | -24 | -50 | -10 | -44 |
| x |
LPK+19 (mouse 3T3-L1 preadipocytes)
|
76 | 105 | -32 | -38 | 18 | -108 |
| y |
LPK+19 (mouse 3T3-L1 adipocytes)
|
97 | 208 | -58 | 18 | -147 | -59 |
| z |
LPK+19 (mouse 3T3-L1 macrophages)
|
220 | 134 | -1 | 26 | -130 | -32 |
| A |
DKM+20 (bone marrow-derived MSCs aggregates)
|
57 | 117 | -31 | -21 | -234 | -37 |
Gene names or other identifiers were converted to UniProt accession numbers using the UniProt mapping tool.
a. Gene names from Supporting Information Table 1S of Pruksakorn et al. (2010). b. c. Sheets 2 and 3 in Table S1 of Morrison et al. (2012). d. e. Supplemental Table 1C of McMahon et al. (2012), filtered to include proteins with expression ratios < 0.77 or > 1.3. f. Supplemental Table S5 of Yan et al. (2013). g. h. Supplemental Table S4 of Zanivan et al. (2013). i. Table S1 of He et al. (2014). j. k. l. Supplemental Table S1 of Konze et al. (2014) (hESC: human embryonic stem cells; hiPSC: human induced pluripotent stem cells; hPSC: human pluripotent stem cells). m. Table S2 of Rajcevic et al. (2014), filtered to include proteins that have differences in spectral counts recorded in at least two of three experiments, absolute overall fold change is ≥ 1.5 or ≤ 2/3, and p-value is < 0.05. n. Supplementary Figure 2 of Saini et al. (2014). o. P1_Data sheet in the Supporting Information file of Wrzesinski et al. (2014). p. Supplemental Table S1 of Musrap et al. (2015), filtered to exclude marked contaminants and reverse sequences and to include proteins with “Ratio H/L normalized” > 1.5 or < 2/3. q. Tables S1a and S1b of Yue et al. (2016). r. Tables S2 and S3 of Kim et al. (2018). s. t. Supplementary Table 3 of Toelle, Gaggioli & Dengjel (2018). u. Extracted from proteinGroups.txt in ProteomeXchange Dataset PXD008244/txt.zip (Erhart et al., 2019), including proteins quantified in at least two replicates in each condition (adherent and spheroid) and with median fold change > 2 or < 0.5. v. Extracted from Supplementary Table 1 of Gęgotek et al. (2019). Values were quantile normalized, then ratios were calculated between 3D and 2D cultures for each treatment (control, CBD, UVA, UVA+CBD, UVB, UVB+CBD). Ratios > 1.2 or < 1/1.2 in at least 4 treatments were used to identify differentially expressed proteins. w. Supplementary Data I, sheet “Volcano plot 2Dv3D” of Hurrell, Lilley & Cromarty (2019). x. y. z. Supporting Table 1 of Lee et al. (2019), sheets “3P2P” (mono-cultured preadipocytes), “3A2A” (mono-cultured adipocytes), “3C2C” (co-cultured adipocytes with macrophages), filtered to include proteins marked as “T-test Significant” and with absolute value of “N: T-test Difference” > log2(0.5). A. Supplementary Table S2 of Doron et al. (2020), filtered to include proteins with fold change > 2 or < 0.5 for all donors.
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