This vignette from the R package JMDplots version 1.2.19-9 shows chemical metrics for proteins 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 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, 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 |
PNWB09 (Synechocystis sp. PCC6803 in 6% w/v NaCl vs no added salt)
|
77 | 55 | 4 | 25 | -8 | 27 | 72 | -120 |
| b |
FTR+10 (Corynebacterium glutamicum in 750 mM NaCl vs control medium)
|
27 | 65 | 2 | 15 | -44 | -119 | 127 | 97 |
| c |
LPK+13 (Lactobacillus johnsonii with vs without 0.1-0.3% bile salt)
|
123 | 88 | 26 | -65 | -68 | 67 | 78 | -62 |
| d |
QHT+13 (Synechocystis sp. PCC 6803 Protein in 4% w/v vs 0% added NaCl for 24 h)
|
42 | 26 | -42 | -54 | -150 | 111 | -44 | 48 |
| e |
QHT+13 (Synechocystis sp. PCC 6803 Protein in 4% w/v vs 0% added NaCl for 48 h)
|
46 | 62 | -17 | 29 | -25 | 3 | -192 | -46 |
| f |
ADW+14 (Bifidobacterium longum BBMN68 Protein with vs without 0.75 g/l ox bile)
|
20 | 24 | 8 | 6 | 34 | 28 | 75 | -84 |
| g |
KKG+14 (Escherichia coli Protein in NaCl (0.967 aw) vs control for immediate)
|
30 | 158 | -12 | -19 | 33 | 121 | 168 | 123 |
| h |
KKG+14 (Escherichia coli Protein in NaCl (0.967 aw) vs control for 30 min)
|
21 | 162 | -15 | -20 | 76 | 140 | 122 | 139 |
| i |
KKG+14 (Escherichia coli Protein in NaCl (0.967 aw) vs control for 80 min)
|
37 | 126 | -29 | -28 | 100 | 161 | 82 | 175 |
| j |
KKG+14 (Escherichia coli Protein in NaCl (0.967 aw) vs control for 310 min)
|
12 | 399 | -2 | -31 | 57 | 48 | 130 | 127 |
| k |
PBP+14 (Listeria monocytogenes in 3% NaCl vs control at 4.C)
|
54 | 86 | 16 | 1 | -16 | -50 | -48 | -86 |
| l |
PBP+14 (Listeria monocytogenes in 3% NaCl vs control at 37.C)
|
60 | 25 | 3 | 3 | -4 | -16 | 18 | -49 |
| m |
KLB+15 (Caulobacter crescentus Protein in 200 mM sucrose vs M2 minimal salts medium)
|
33 | 33 | 20 | -60 | 61 | 55 | 10 | -35 |
| n |
KLB+15 (Caulobacter crescentus Protein in 40/50 mM NaCl vs M2 minimal salts medium)
|
33 | 27 | 19 | -48 | 70 | 75 | -2 | -80 |
| o |
SKV+16 (Escherichia coli in Glucose vs LB)
|
743 | 282 | 5 | -13 | -8 | 14 | 2 | -43 |
| p |
SKV+16 (Escherichia coli in Osmotic.stress.glucose vs LB)
|
978 | 343 | 6 | -8 | -21 | -19 | -50 | -73 |
| q |
KAK+17 (Lactobacillus fermentum with vs without 1.2% w/v bile salts)
|
106 | 81 | 34 | -37 | -418 | 30 | 48 | -142 |
| r |
LYS+17 (Lactobacillus salivarius LI01 with vs without 0.15% ox bile)
|
177 | 205 | 2 | -37 | 18 | 78 | 14 | 76 |
| s |
HGC+18 (Lactobacillus casei BL23 in hyper-concentrated vs isotonic sweet whey)
|
116 | 64 | 13 | -51 | -54 | -15 | 33 | 1 |
| t |
KSK+18 (Acidihalobacter prosperus DSM 14174 30 g/L / 5 g/L NaCl)
|
292 | 316 | -7 | 11 | -8 | 31 | -102 | -45 |
| u |
LJC+18 (Listeria monocytogenes WT in 0.5 M NaCl vs control medium)
|
65 | 66 | -20 | -9 | -40 | 106 | 31 | 46 |
| v |
LJC+18 (Listeria monocytogenes mutant in 0.5 M NaCl vs control medium)
|
37 | 30 | -13 | -11 | 42 | 127 | -93 | 99 |
| w |
TSC18 (Caulobacter crescentus WT in 300 mM sucrose vs control)
|
91 | 28 | 5 | 2 | -95 | 36 | -207 | -16 |
| x |
TSC18 (Caulobacter crescentus GsrN in 300 mM sucrose vs control)
|
99 | 107 | 2 | 19 | -78 | -7 | -244 | -29 |
| y |
LWS+19 (Lactobacillus plantarum FS5-5 in 6-8% w/v vs 0% NaCl)
|
72 | 46 | 14 | -42 | -81 | -48 | 10 | 59 |
| z |
MGF+19 (Staphylococcus aureus in 10% vs 0% NaCl)
|
88 | 58 | 33 | -38 | -211 | 58 | -114 | -32 |
| A |
MGF+19 (Staphylococcus aureus in 20% vs 0% NaCl)
|
184 | 99 | 24 | 4 | -133 | 12 | -120 | -148 |
| B |
AST+20 (Lactobacillus fermentum with vs without 0.3% to 1.5% w/v bile salts)
|
368 | 378 | -2 | -4 | -36 | -2 | 28 | 16 |
| C |
GBR+20 (Propionibacterium freudenreichii CIRM129 in NaCl vs MMO)
|
90 | 74 | -15 | 35 | 25 | -104 | -50 | 138 |
| D |
GBR+20 (Propionibacterium freudenreichii CIRM1025 in NaCl vs MMO)
|
64 | 78 | -9 | 13 | 11 | -37 | -82 | 127 |
a. Additional file 3: Table S2 of Pandhal et al. (2009). b. Supplementary Table 8 of Fränzel et al. (2010). Only proteins with consistent expression ratios (all > 1 or all < 1) at each time point (15, 60, and 180 min.) were included. c. Supporting Information Table 1 of Lee et al. (2013) (sheets “Up-Down Proteins” and “Unknown function”). d. e. Supplementary Tables S3A and S3B of Qiao et al. (2013). f. Table 1 (proteins) and supplemental Table S2 (genes) of An et al. (2014). g. h. i. j. Supporting Information Table S2 of Kocharunchitt et al. (2014). k. l. Supporting Information Table of Pittman et al. (2014), filtered to include proteins with p-value < 0.05. m. n. Additional file Table S2 of Kohler et al. (2015). o. p. Supplementary Table S6 of Schmidt et al. (2016), filtered to include proteins with fold change > 2 or < 0.5 for the ratios Glucose / LB (lysogeny broth) or Osmotic-stress glucose / LB. q. Supplementary Table 1 (sheets “0.76 fold down regulated” and “1.3 fold up regulated”) of Kaur et al. (2017). r. Supplemental Table S-2 of Lv et al. (2017), filtered to include proteins with log2 fold change > 1 or < -1 and p-value < 0.05. s. Supplementary Figure 1 of Huang et al. (2018). t. Supplementary Table 1 of Khaleque et al. (2018) (amino acid compositions computed from protein sequences in the list of gene annotations). u. v. Tables S1–S6 of Lee et al. (2018). For each of the wild-type and ∆sigB mutant, only proteins that were identified in multicellular vesicles in a single condition (0.5 M salt stress or without salt stress) were included. w. x. Extracted from proteinGroups.txt in PRIDE project PXD010072/MaxQuantOutput.tar.gz (Tien, Stein & Crosson, 2018), filtered to include proteins with non-zero LFQ intensity values for all replicates in each experiment; the medians of these values were used to compute fold changes; proteins with fold change > 1.5 or < 2/3 were kept. y. Table 2 of Li et al. (2019). z. A. Supplementary Tables S4 and S5 of Ming et al. (2019), filtered to include proteins with fold change >= 2 or <= 0.5. B. Supplementary Table 1 (sheets “>2.0 Fold” and “< 0.5 Fold”) of Ali et al. (2020). C. D. Supplementary Table 1 of Gaucher et al. (2020) (column “MMO+NaCl/MMO” for CIRM129 and CIRM1025).
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