Yeast Gene Expression in Hyper- and Hypo-osmotic Shock

This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins coded by genes that are differentially expressed in hyperosmotic and hypoosmotic shock in yeast. 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_yeast_stress(2020)

Differences are calculated as (median value for proteins coded by up-regulated genes) - (median value for proteins coded by down-regulated genes). Circles and squares stand for hyperosmotic and hypoosmotic experiments, respectively.

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

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

pI – isoelectric point; GRAVY – grand average of hydropathicity.

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

set	reference (description)	n_down	n_up	ΔZ_C	Δn_H₂O	ΔpI	ΔGRAVY	Δn_AA	ΔMW
a	`GSK+00` (yeast transcriptome in 1M sorbitol at 5 min)	141	212	14	-55	-7	110	-70	-45
b	`GSK+00` (yeast transcriptome in 1M sorbitol at 15 min)	802	923	1	-44	-15	24	66	42
c	`GSK+00` (yeast transcriptome in 1M sorbitol at 30 min)	430	613	1	-44	-133	-15	44	31
d	`GSK+00` (yeast transcriptome in 1M sorbitol at 45 min)	84	286	-5	-40	-166	9	-87	-5
e	`GSK+00` (yeast transcriptome in 1M sorbitol at 60 min)	30	98	9	-7	16	-51	-20	12
f	`GSK+00` (yeast transcriptome in 1M sorbitol at 90 min)	73	153	-34	-23	-19	192	102	-56
g	`GSK+00` (yeast transcriptome in 1M sorbitol at 120 min)	119	220	-7	-19	-7	-36	104	63
h	`GSK+00` (yeast transcriptome in hypoosmotic shock at 5 min)	292	332	11	3	-195	-6	186	-129
i	`GSK+00` (yeast transcriptome in hypoosmotic shock at 15 min)	479	459	6	45	-177	-62	202	-38
j	`GSK+00` (yeast transcriptome in hypoosmotic shock at 30 min)	718	386	10	39	-128	-85	198	-18
k	`GSK+00` (yeast transcriptome in hypoosmotic shock at 45 min)	502	327	11	32	-138	-76	304	-1
l	`GSK+00` (yeast transcriptome in hypoosmotic shock at 60 min)	312	258	6	30	-89	-95	368	44

set

reference (description)

n_down

n_up

ΔZ_C

Δn_H₂O

ΔpI

ΔGRAVY

Δn_AA

ΔMW

GSK+00 (yeast transcriptome in 1M sorbitol at 5 min)

141

212

-55

-7

110

-70

-45

GSK+00 (yeast transcriptome in 1M sorbitol at 15 min)

802

923

-44

-15

GSK+00 (yeast transcriptome in 1M sorbitol at 30 min)

430

613

-44

-133

-15

GSK+00 (yeast transcriptome in 1M sorbitol at 45 min)

286

-5

-40

-166

-87

-5

GSK+00 (yeast transcriptome in 1M sorbitol at 60 min)

-7

-51

-20

GSK+00 (yeast transcriptome in 1M sorbitol at 90 min)

153

-34

-23

-19

192

102

-56

GSK+00 (yeast transcriptome in 1M sorbitol at 120 min)

119

220

-7

-19

-7

-36

104

GSK+00 (yeast transcriptome in hypoosmotic shock at 5 min)

292

332

-195

-6

186

-129

GSK+00 (yeast transcriptome in hypoosmotic shock at 15 min)

479

459

-177

-62

202

-38

GSK+00 (yeast transcriptome in hypoosmotic shock at 30 min)

718

386

-128

-85

198

-18

GSK+00 (yeast transcriptome in hypoosmotic shock at 45 min)

502

327

-138

-76

304

-1

GSK+00 (yeast transcriptome in hypoosmotic shock at 60 min)

312

258

-89

-95

368

Data Sources

a. – l. complete_dataset.txt of Gasch et al. (2000), filtered to include genes with an expression ratio > log₂(1.5) or < log₂(1/1.5) at any time in the “1M sorbitol” or “Hypo-osmotic shock” experiments.

References

Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Molecular Biology of the Cell 11:4241–4257. DOI: 10.1091/mbc.11.12.4241.

JMDplots vignettes

Yeast Gene Expression in Hyper- and Hypo-osmotic Shock

Data Sources

References