This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins that are differentially expressed in lung 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 |
LXC+06 (SCC / NBE)
|
22 | 44 | 19 | 36 | -65 | -38 |
| b |
KHA+12 (ADC / pooled normal)
|
25 | 25 | -27 | 7 | 185 | 163 |
| c |
KHA+12 (SCC / pooled normal)
|
23 | 24 | -55 | 7 | -68 | 309 |
| d |
YLL+12 (LCM SCC / NBE)
|
47 | 46 | -3 | 29 | 21 | -82 |
| e |
ZZD+12 (LCM LSCC / NBE)
|
54 | 41 | 3 | -2 | 85 | -21 |
| f |
ZZY+13 (plasma membrane ADC / ANT)
|
24 | 21 | 37 | 19 | 328 | -260 |
| g |
LLY+14 (SCC / normal)
|
29 | 48 | -1 | 38 | -24 | -73 |
| h |
LWT+14 (NSCLC / ANT)
|
345 | 1240 | -9 | 31 | -27 | 68 |
| i |
ZLH+14 (membrane microdissected ADC / ANT)
|
310 | 257 | -2 | 66 | -56 | 71 |
| j |
ZLS+14 (endothelial SCC / normal)
|
61 | 24 | 28 | 37 | 19 | -108 |
| k |
KNT+15 (FFPE LPIA / pseudo-normal)
|
346 | 66 | 24 | -12 | 134 | -150 |
| l |
BLL+16 (NSCLC proteome)
|
354 | 240 | 7 | -31 | -132 | 29 |
| m |
FGP+16 (adenocarcinoma / ANT)
|
81 | 285 | -20 | 43 | -121 | 33 |
| n |
JCP+16 (mouse endothelial tumor / normal)
|
18 | 28 | -21 | 44 | 65 | -21 |
| o |
HHH+16 (pN0 / normal)
|
210 | 135 | -21 | 42 | -52 | 37 |
| p |
HHH+16 (pN1 / normal)
|
233 | 170 | -20 | 35 | -96 | 63 |
| q |
HHH+16 (pN2.M1 / normal)
|
154 | 158 | -17 | 17 | -18 | 118 |
| r |
TLB+16 (NSCLC / ANT)
|
346 | 1059 | -6 | 12 | -146 | 9 |
| s |
FGW+17 (adenocarcinoma / ANT)
|
71 | 1031 | -26 | 21 | -522 | 77 |
| t |
LZW+17 (mitochondria-related proteins adenocarcinoma / normal)
|
30 | 30 | -10 | 34 | -21 | 84 |
| u |
SFS+17 (SCC / ANT LF)
|
422 | 311 | -2 | 1 | -96 | 10 |
| v |
WLC+17 (NSCLC / ANT)
|
20 | 71 | -14 | 57 | 90 | 18 |
| w |
YCC+17 (SCC.Oncogene / ANT)
|
280 | 115 | 2 | -4 | -160 | -41 |
| x |
YCC+17 (SCC.TSG / ANT)
|
207 | 69 | -17 | 20 | -214 | 43 |
| y |
YCC+17 (SCC.Glycoprotein / ANT)
|
64 | 86 | 6 | 2 | 73 | 21 |
| z |
YCC+17 (ADC.Oncogene / ANT)
|
385 | 72 | -15 | 17 | -146 | -26 |
| A |
YCC+17 (ADC.TSG / ANT)
|
286 | 42 | -14 | 30 | -190 | 56 |
| B |
YCC+17 (ADC.Glycoprotein / ANT)
|
83 | 134 | -6 | -34 | -96 | 145 |
| C |
KPS+20 (ADC / adjacent normal early)
|
86 | 279 | 8 | 14 | 73 | 68 |
| D |
KPS+20 (ADC / adjacent normal advanced)
|
92 | 274 | -6 | -1 | 58 | 22 |
| E |
XZW+20 (ADC / non-cancerous adjacent)
|
603 | 2735 | -14 | 13 | -129 | 61 |
Where given, 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 of Li et al. (2006). b. c. Gene names from Tables II and III of Kikuchi et al. (2012). d. Gene names from Table 2 of Yan et al. (2012). e. IPI numbers from Table 1 of Zeng et al. (2012). f. Table 2 of Zhang et al. (2013). g. Table 1 of Lihong et al. (2014). h. Supplementary data 1b of Li et al. (2014). i. Supplementary Data of Zhang et al. (2014). j. Gene names from Supporting Information Table S5 of Zhuo et al. (2014) (differential expression between normal endothelial cells and both paratumor and tumor endothelial cells). k. Table S3 of Kato et al. (2015) (LPIA: lepidic predominant invasive adenocarcinoma vs pN: pseudo-normal), filtered to include proteins with log2 fold change > 1 or < -1 and p-value < 0.05. l. UniProt names from Table S2 of Backes et al. (2016), filtered to include proteins with log2 fold change > 1.5 or < -1/1.5 and p-value < 0.05. m. Gene names from Table S2 of Fahrmann et al. (2016). n. Gene names from Table 1 of Jin et al. (2016). o. p. q. Supplemental Table S3B of Hsu et al. (2016) (primary tumor / normal comparison; pN0: no nodes involved; pN1: ipsilateral peribronchial/interlobar/hilar LN metastasis; pN2: ipsilateral mediastinal LN metastasis; M1: distant metastasis or malignant effusion). r. Supplemental Table 2 of Tenzer et al. (2016), filtered with adjusted p-value < 0.05 and fold change ≥ 1.5 or ≤ 2/3. s. Gene names from Supplementary Table S1 of Fahrmann et al. (2017), filtered with p-value < 0.05. t. Table 1 of Li et al. (2017). u. Supplementary Table S2 of Stewart et al. (2017) (sheet LF: label-free quantification). v. Supplementary Table 1 of Wang et al. (2017). w. x. y. z. A. B. Gene names from Tables S2–S6 of Yang et al. (2017) filtered to keep proteins with fold change ≥1.5 or ≤2/3 (Oncogene: oncogene-coded proteins; TSG: tumor suppressor gene-coded proteins; Glycoprotein: glycoproteomics data). C. D. Supplemental Table S2 of Kelemen et al. (2020) for early (stage I-II) and advanced (stage III-IV) adenocarcinomas. E. Gene names from Table S4D and UniProt IDs from Table S4A of Xu et al. (2020).
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