Chemical analysis of The Cancer Genome Atlas

This vignette from the R package JMDplots version 1.2.17-10 shows chemical metrics for proteins associated with transcripts that are differentially expressed in cancer compared to normal tissue (data from The Cancer Genome Atlas and Genotype-Tissue Expression Project via GEPIA2). The analysis is described in more detail in a paper (Dick, 2021). Abbreviations:

Z_C – average oxidation state of carbon.

n_H₂O – stoichiometric hydration state per residue (Dick et al., 2020) computed using the QEC basis species (glutamine, glutamic acid, cysteine, H₂O, O₂).

datasets <- pdat_TCGA()

Differences are calculated as (median value for up-regulated proteins) - (median value for down-regulated proteins). Dashed lines enclose the 50% credible region for highest probability density.

In the table, values of ΔZ_C and Δn_H₂O are multiplied by 1000, values of ΔMW are multiplied by 100, and negative values are shown in bold. Abbreviations:

n_down – number of down-regulated proteins; n_up – number of up-regulated proteins.

n_AA – protein length; MW – molecular weight per residue.


set	reference (description)	n_down	n_up	ΔZ_C	Δn_H₂O	Δn_AA	ΔMW
a	`GEPIA2` (ACC)	2013	391	-9	14	-207	8
b	`GEPIA2` (BLCA)	1722	735	-18	27	-114	20
c	`GEPIA2` (BRCA)	1749	1256	-15	13	-89	40
d	`GEPIA2` (CESC)	2972	1627	-21	17	-159	28
e	`GEPIA2` (COAD)	2165	2327	-21	12	-108	32
f	`GEPIA2` (DLBC)	771	7887	5	15	-6	88
g	`GEPIA2` (ESCA)	1088	2401	-1	9	100	61
h	`GEPIA2` (GBM)	1883	4642	-12	-6	-107	90
i	`GEPIA2` (HNSC)	557	1385	3	-3	44	27
j	`GEPIA2` (KICH)	3002	615	-8	0	-9	3
k	`GEPIA2` (KIRC)	1141	1433	5	3	-43	-5
l	`GEPIA2` (KIRP)	1258	827	-3	1	-52	35
m	`GEPIA2` (LAML)	2578	2490	9	-17	174	10
n	`GEPIA2` (LGG)	1376	3500	-6	-2	-14	80
o	`GEPIA2` (LIHC)	570	1342	-4	19	-116	79
p	`GEPIA2` (LUAD)	2430	949	-14	5	-162	-21
q	`GEPIA2` (LUSC)	3167	1654	-12	9	-143	17
r	`GEPIA2` (OV)	3567	2241	-15	5	-205	-56
s	`GEPIA2` (PAAD)	335	8167	4	14	-26	80
t	`GEPIA2` (PRAD)	1778	518	-34	5	-134	52
u	`GEPIA2` (READ)	2331	2455	-22	11	-109	45
v	`GEPIA2` (SKCM)	3007	2252	-16	7	-102	41
w	`GEPIA2` (STAD)	708	3458	-2	8	-4	63
x	`GEPIA2` (TGCT)	6227	2174	-12	1	-127	-19
y	`GEPIA2` (THCA)	2341	524	-16	6	-182	-22
z	`GEPIA2` (THYM)	783	10099	9	15	44	74
A	`GEPIA2` (UCEC)	3834	1733	-18	12	-214	-24
B	`GEPIA2` (UCS)	3418	1592	-13	14	-212	-24

set

reference (description)

n_down

n_up

ΔZ_C

Δn_H₂O

Δn_AA

ΔMW

GEPIA2 (ACC)

2013

391

-9

-207

GEPIA2 (BLCA)

1722

735

-18

-114

GEPIA2 (BRCA)

1749

1256

-15

-89

GEPIA2 (CESC)

2972

1627

-21

-159

GEPIA2 (COAD)

2165

2327

-21

-108

GEPIA2 (DLBC)

771

7887

-6

GEPIA2 (ESCA)

1088

2401

-1

100

GEPIA2 (GBM)

1883

4642

-12

-6

-107

GEPIA2 (HNSC)

557

1385

-3

GEPIA2 (KICH)

3002

615

-8

-9

GEPIA2 (KIRC)

1141

1433

-43

-5

GEPIA2 (KIRP)

1258

827

-3

-52

GEPIA2 (LAML)

2578

2490

-17

174

GEPIA2 (LGG)

1376

3500

-6

-2

-14

GEPIA2 (LIHC)

570

1342

-4

-116

GEPIA2 (LUAD)

2430

949

-14

-162

-21

GEPIA2 (LUSC)

3167

1654

-12

-143

GEPIA2 (OV)

3567

2241

-15

-205

-56

GEPIA2 (PAAD)

335

8167

-26

GEPIA2 (PRAD)

1778

518

-34

-134

GEPIA2 (READ)

2331

2455

-22

-109

GEPIA2 (SKCM)

3007

2252

-16

-102

GEPIA2 (STAD)

708

3458

-2

-4

GEPIA2 (TGCT)

6227

2174

-12

-127

-19

GEPIA2 (THCA)

2341

524

-16

-182

-22

GEPIA2 (THYM)

783

10099

GEPIA2 (UCEC)

3834

1733

-18

-214

-24

GEPIA2 (UCS)

3418

1592

-13

-212

-24

Data Sources

a. – B. GEPIA2 (Tang et al., 2019).

References

Tang Z, Kang B, Li C, Chen T, Zhang Z. 2019. GEPIA2: An enhanced web server for large-scale expression profiling and interactive analysis. Nucleic Acids Research 47:W556–W560. DOI: 10.1093/nar/gkz430.