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 compared to control conditions. The analysis is described in more detail in a paper (Dick et al., 2020). Abbreviations:
Differences are calculated as (median value for proteins coded by up-regulated genes) - (median value for proteins coded by down-regulated genes). Dashed lines enclose the 50% credible region for highest probability density.
In the table, values of ΔZC, ΔnH2O, and ΔGRAVY are multiplied by 1000, values of ΔpI and ΔMW are multiplied by 100, and negative values are shown in bold. Abbreviations:
| set | reference (description) | ndown | nup | ΔZC | ΔnH2O | ΔpI | ΔGRAVY | ΔnAA | ΔMW |
|---|---|---|---|---|---|---|---|---|---|
| a |
KSA+02 (Synechocystis sp. PCC 6803 in 0.5 M NaCl vs control)
|
36 | 62 | 8 | 15 | 28 | 62 | 33 | -106 |
| b |
KSA+02 (Synechocystis sp. PCC 6803 in 0.5 M sorbitol vs control)
|
32 | 45 | -3 | -6 | 25 | -16 | -2 | 52 |
| c |
WJ02 (Escherichia coli in 0.4 M NaCl vs control)
|
102 | 41 | 9 | 1 | 8 | -8 | -32 | 15 |
| d |
HZP+05 (Yersinia pestis in 0.5 M NaCl vs control)
|
13 | 103 | -6 | -24 | -38 | -11 | 55 | 144 |
| e |
HZP+05 (Yersinia pestis in 0.5 M sorbitol vs control)
|
40 | 103 | 11 | -44 | -36 | -65 | 181 | 123 |
| f |
LGW+05 (Shewanella oneidensis MR-1 in 0.5 vs 0.1 M NaCl)
|
563 | 541 | 2 | 15 | -6 | 7 | -19 | -46 |
| g |
SLA+05 (Synechocystis sp. PCC 6803 in 0.5 M sorbitol vs control)
|
27 | 53 | 19 | 26 | -62 | -74 | 103 | 92 |
| h |
GCP08 (Escherichia coli in 0.5 M vs 0 M NaCl at 30 deg C)
|
307 | 40 | 11 | 5 | -35 | -64 | 168 | -155 |
| i |
GCP08 (Escherichia coli in 0.5 M vs 0 M NaCl at 43 deg C)
|
89 | 144 | 1 | -7 | -12 | 2 | 96 | -40 |
| j |
SBB+09 (Escherichia coli in ~2.7 Os/kg NaCl vs control)
|
35 | 26 | -34 | 25 | -47 | 150 | -115 | 5 |
| k |
SBB+09 (Escherichia coli in ~2.7 Os/kg sucrose vs control)
|
28 | 37 | -32 | 28 | 26 | 151 | 72 | 14 |
| l |
HMO+10 (Bacillus subtilis in 6% w/v NaCl vs control)
|
417 | 459 | -2 | 1 | 30 | -8 | -33 | 73 |
| m |
BBWB12 (Listeria monocytogenes strain H7858 in 6% NaCl at 2.5% lag-phase duration)
|
18 | 55 | 16 | 49 | -51 | -74 | -18 | -235 |
| n |
BBWB12 (Listeria monocytogenes strain H7858 in 6% NaCl at 5% lag-phase duration)
|
85 | 134 | 7 | -15 | -64 | -10 | -70 | -50 |
| o |
BBWB12 (Listeria monocytogenes strain H7858 in 6% NaCl at 10% lag-phase duration)
|
136 | 156 | 7 | -18 | -65 | 24 | -65 | -104 |
| p |
BBWB12 (Listeria monocytogenes strain H7858 in 6% NaCl at 20% lag-phase duration)
|
58 | 44 | 2 | 8 | -42 | 129 | 39 | -268 |
| q |
LB12 (Synechococcus sp. strain PCC 7002 in 1.5 M NaCl vs control)
|
311 | 646 | 6 | 11 | -61 | 41 | 2 | -150 |
| r |
QHT+13 (Synechocystis sp. PCC 6803 Gene in 4% w/v vs 0% added NaCl for 24 h)
|
50 | 48 | 13 | 56 | 111 | 39 | 74 | -194 |
| s |
QHT+13 (Synechocystis sp. PCC 6803 Gene in 4% w/v vs 0% added NaCl for 48 h)
|
50 | 50 | -7 | -49 | 76 | 27 | -12 | 56 |
| t |
QHT+13 (Synechocystis sp. PCC 6803 Gene in 4% w/v vs 0% added NaCl for 72 h)
|
50 | 49 | -20 | 5 | 152 | 156 | 68 | -30 |
| u |
WGB+13 (Escherichia coli in 0.3 M NaCl vs control)
|
525 | 524 | 12 | -46 | 66 | 55 | -34 | 65 |
| v |
WGB+13 (Escherichia coli in 0.6 M urea vs control)
|
337 | 370 | -1 | 5 | 152 | -36 | -74 | 130 |
| w |
ADW+14 (Bifidobacterium longum BBMN68 Gene with vs without 0.75 g/l ox bile)
|
160 | 76 | 12 | -51 | -30 | -169 | -46 | 202 |
| x |
KKG+14 (Escherichia coli Gene in NaCl (0.967 aw) vs control for 30 min)
|
15 | 164 | 3 | 26 | -65 | 122 | 7 | -58 |
| y |
KKG+14 (Escherichia coli Gene in NaCl (0.967 aw) vs control for 80 min)
|
409 | 727 | 11 | -16 | 19 | -54 | -35 | 83 |
| z |
KKG+14 (Escherichia coli Gene in NaCl (0.967 aw) vs control for 310 min)
|
319 | 571 | 7 | -21 | -8 | -71 | -38 | 74 |
| A |
KSM+14 (Bacillus subtilis in 1.2 M NaCl vs control)
|
687 | 642 | -6 | -7 | 11 | 63 | 4 | 6 |
| B |
KSM+14 (Bacillus subtilis with vs without glycine betaine in 1.2 M NaCl)
|
311 | 559 | 8 | 10 | -21 | -16 | 4 | -41 |
| C |
MGM+14 (Escherichia coli in 3.5 vs 2% NaCl (with glycine betaine))
|
169 | 64 | 7 | -13 | 25 | -5 | 11 | 15 |
| D |
MGM+14 (Escherichia coli in 4.5 vs 2% NaCl (with glycine betaine))
|
740 | 579 | -9 | -30 | 60 | 167 | 56 | -65 |
| E |
MGM+14 (Escherichia coli in 5 vs 2% NaCl (with glycine betaine))
|
43 | 82 | 8 | -14 | 34 | -99 | 36 | 68 |
| F |
MGM+14 (Escherichia coli in 5.5 vs 2% NaCl (with glycine betaine))
|
79 | 84 | 15 | -11 | 30 | -16 | -18 | -22 |
| G |
SLM+14 (Enterococcus faecalis in 6.5% NaCl vs control at 5 min)
|
113 | 69 | -6 | -17 | 74 | 79 | 82 | -4 |
| H |
SLM+14 (Enterococcus faecalis in 6.5% NaCl vs control at 30 min)
|
125 | 175 | -4 | -27 | 48 | -2 | -39 | 166 |
| I |
SLM+14 (Enterococcus faecalis in 6.5% NaCl vs control at 60 min)
|
170 | 172 | 3 | -57 | -152 | 47 | 67 | 16 |
| J |
FRH+15 (Salmonella enterica in NaCl vs control for 1h h)
|
113 | 60 | 16 | 81 | -185 | 55 | 72 | -357 |
| K |
FRH+15 (Salmonella enterica in NaCl vs control for 6h h)
|
255 | 149 | 7 | 25 | -7 | -11 | 62 | -133 |
| L |
FRH+15 (Salmonella enterica in NaCl vs control for 24h h)
|
163 | 60 | 0 | -48 | 35 | -66 | -51 | 125 |
| M |
FRH+15 (Salmonella enterica in KCl vs control for 1h h)
|
92 | 45 | 13 | 59 | -214 | 19 | 105 | -343 |
| N |
FRH+15 (Salmonella enterica in KCl vs control for 6h h)
|
349 | 264 | 3 | 3 | -10 | -80 | -18 | 40 |
| O |
FRH+15 (Salmonella enterica in KCl vs control for 24h h)
|
403 | 182 | 15 | -21 | -12 | -53 | 66 | -13 |
| P |
FRH+15 (Salmonella enterica in glycerol vs control for 1h h)
|
300 | 333 | -8 | 12 | 11 | 6 | -18 | 10 |
| Q |
FRH+15 (Salmonella enterica in glycerol vs control for 6h h)
|
261 | 132 | -18 | -35 | 46 | 60 | -50 | 109 |
| R |
FRH+15 (Salmonella enterica in glycerol vs control for 24h h)
|
164 | 67 | 0 | -52 | 27 | -35 | -41 | 90 |
| S |
KLB+15 (Caulobacter crescentus Gene in 40/50 mM NaCl vs M2 minimal salts medium)
|
209 | 142 | 9 | -45 | 47 | 109 | -8 | -125 |
| T |
KLB+15 (Caulobacter crescentus Gene in 200 mM sucrose vs M2 minimal salts medium)
|
105 | 96 | 27 | -65 | -70 | 73 | 42 | -100 |
| U |
HLL17 (Methylocystis sp. strain SC2 in 0.75% NaCl vs control at 45min)
|
105 | 46 | -7 | 42 | 170 | 179 | -11 | -187 |
| V |
HLL17 (Methylocystis sp. strain SC2 in 0.75% NaCl vs control at 14h)
|
22 | 75 | 22 | -34 | -195 | 154 | 16 | -39 |
| W |
MWZ+18 (Lactobacillus paracasei L9 with vs without 0.13% ox bile)
|
42 | 56 | 2 | -35 | -4 | -57 | -22 | 12 |
a. b. Tables 1–2 of Kanesaki et al. (2002). c. Table 1 of Weber & Jung (2002). d. e. Table 3 of Han et al. (2005). f. Table 1S of Liu et al. (2005). g. Tables 2–3 of Shapiguzov et al. (2005). h. i. Dataset.txt of Gunasekera, Csonka & Paliy (2008). j. k. Table 3 of Shabala et al. (2009). l. Table S2 (sheet “S2_Table_3”) of Hahne et al. (2010). m. n. o. p. Table S5 of Bergholz et al. (2012), filtered to include genes with log2 fold change > 1 or < -1. q. Table S2 of Ludwig & Bryant (2012), filtered to include genes with p-value < 0.05 and fold change > 2 or < 0.5. r. s. t. Supplementary Tables S2A–S2F of Qiao et al. (2013). u. v. Dataset.txt of Withman et al. (2013), filtered to include proteins with log fold change (column “N vs K Wmean [M]” for NaCl and “U vs K Wmean [M]” for urea) > 1 or < 1 and p-value less than 0.05. w. Table S2 of An et al. (2014) x. y. z. Table S2 of Kocharunchitt et al. (2014) A. B. Tables S5–S6 of Kohlstedt et al. (2014). C. D. E. F. Supplemental Table S1 of Metris et al. (2014), filtered to include genes with differences of Normalized ln(cDNA/gDNA) > 1 or < 1 between 2 % and higher NaCl concentration. G. H. I. Table S2 of Solheim et al. (2014). J. K. L. M. N. O. P. Q. R. Tables S1–S3 of Finn et al. (2015). S. T. Table S2 of Kohler et al. (2015). U. V. Tables S5–S8 of Han, Link & Liesack (2017). W. Table S6 of Ma et al. (2018).
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