Work Description

Title: Dataset Associated with "Thermodynamics and Selection of the Plasminogen Activator Inhibitor-1 Latency Transition" Open Access Deposited

h
Attribute Value
Methodology
  • This data set was collected using phage display of a comprehensive PAI-1 variant library that was screened for its ability to inhibit its target serine protease uPA after 0h and 48h incubation at 37C to identify PAI-1 variants that affect the thermodynamic stability of PAI-1. Amino acid substitutions in PAI-1 were identified by sequencing the PAI-1 coding DNA from the input and selected phage using the Illumina DNA sequencing platform. The data are FASTQ files. Bioinformatics scripts to analyze the data are also contained within the repository.
Description
  • A phage displayed amino acid site-saturated variant library of plasminogen activator inhibitor (PAI-1) was screened for thermodynamic functional stability. The data are interpreted in the context of protein evolution and computational variant effect/protein stability predictors. This data set contains FASTQ files of the PAI-1 sequence variants that affect its thermodynamic stability, as well as scripts needed to analyze these files.
Creator
Creator ORCID iD
Depositor
Depositor creator
  • true
Contact information
Discipline
Funding agency
  • National Institutes of Health (NIH)
ORSP grant number
  • AWD026167
Keyword
Citations to related material
  • Haynes LM, Holding ML,Woodard J, Siemieniak D, Ginsburg D. Thermodynamics and selection of the plasminogen activator inhibitor-1 latency transition. bioRxiv [Preprint]. 2025.06.03.655624; doi: https://doi.org/10.1101/2025.06.03.655624
Resource type
Last modified
  • 06/05/2025
Published
  • 06/05/2025
Language
DOI
  • https://doi.org/10.7302/bggn-2y63
License
To Cite this Work:
Haynes, L. M., Holding, M. L., Woodard, J., Siemieniak, D., Ginsburg, D. (2025). Dataset Associated with "Thermodynamics and Selection of the Plasminogen Activator Inhibitor-1 Latency Transition" [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/bggn-2y63

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Files (Count: 29; Size: 46.4 GB)

Thumbnailthumbnail-column Title Original Upload Last Modified File Size Access Actions
PAI-1_THERMODYNAMICS_DATASET_REA...5.txt 2025-06-05 2025-06-05 5.38 KB Open Access
active_3Q02_dG_value.xls 2025-05-22 2025-05-22 428 KB Open Access
Key_to_FASTQ_files.xlsx 2025-05-22 2025-05-22 9.08 KB Open Access
latent_1DVN_dG_value.xls 2025-05-22 2025-05-22 448 KB Open Access
PAI1_human_eve.csv 2025-05-22 2025-05-22 1.14 MB Open Access
latent_1DVN_dG_value.xls 2025-05-22 2025-05-22 448 KB Open Access
GH__5b_VEPs_CI.R 2025-05-22 2025-05-22 3.79 KB Open Access
PAI1_CPT_score.csv 2025-05-22 2025-05-22 193 KB Open Access
phage_code.tar.gz 2025-05-22 2025-05-22 14.4 KB Open Access
GH__6_conServScore_comparison.R 2025-05-22 2025-05-22 9.1 KB Open Access
GH__3_ddG_Compare.R 2025-05-22 2025-05-22 1.61 KB Open Access
data_scores.txt 2025-05-22 2025-05-22 11.1 KB Open Access
GH__1_DeSeq2.R 2025-05-22 2025-05-22 2.77 KB Open Access
GH__4b_ddG_CI.R 2025-05-22 2025-05-22 4.67 KB Open Access
PAI1_alphamissense.txt 2025-05-22 2025-05-22 215 KB Open Access
Sample_4640-LH-1_ACAGTGAT-AGATCTCG.zip 2025-05-28 2025-05-28 5.61 GB Open Access
Sample_4640-LH-1_ACTTGAAT-AGATCTCG.zip 2025-05-28 2025-05-28 3.36 GB Open Access
Sample_4640-LH-1_ATCACGAT-AGATCTCG.zip 2025-05-28 2025-05-28 5.2 GB Open Access
Sample_4640-LH-1_CAGATCAT-AGATCTCG.zip 2025-05-28 2025-05-28 4.87 GB Open Access
Sample_4640-LH-1_CGATGTAT-AGATCTCG.zip 2025-05-28 2025-05-28 6.06 GB Open Access
Sample_4640-LH-1_CTTGTAAT-AGATCTCG.zip 2025-05-28 2025-05-28 5.34 GB Open Access
Sample_4640-LH-1_GCCAATAT-AGATCTCG.zip 2025-05-28 2025-05-28 5.09 GB Open Access
Sample_4640-LH-1_TGACCAAT-AGATCTCG.zip 2025-05-28 2025-05-28 5.39 GB Open Access
Sample_4640-LH-1_TTAGGCAT-AGATCTCG.zip 2025-05-28 2025-05-28 5.5 GB Open Access
GH__4_ddG_lmer_upated.R 2025-06-03 2025-06-03 4.83 KB Open Access
GH__5_VEPs_lmerR_updated.R 2025-06-03 2025-06-03 11.9 KB Open Access
GH__7_compare_to_errorpronePCR.R 2025-06-03 2025-06-03 1.11 KB Open Access
jbc2022_48h_data_filtered.csv 2025-06-03 2025-06-03 158 KB Open Access
WTbg_0h_screen.txt 2025-06-03 2025-06-03 132 KB Open Access

Position FuncCount dnds score bayesfactor
1 5 0.365180467 2.294 0
2 7 0.492097394 1.947 0.535
3 6 1.08762322 6.26 0.291
4 6 0.85255828 3.831 0.022
5 5 0.519671315 2.58 0.012
6 0 0.298035867 -0.011 0.065
7 5 0.508964508 1.466 0.166
8 1 0.478229836 1.368 0.013
9 3 0.180150125 -0.291 0.025
10 5 1.06707086 3.42 0.474
11 1 1.14978903 0.012 5.02
12 1 0.520991053 0.179 0.731
13 0 0.513771186 -0.043 0.401
14 1 0.930970149 -0.03 4.188
15 0 0.009599332 -0.774 0
16 0 0.017767478 -0.774 0
17 0 0.106109325 -0.457 0.005
18 1 0.070850202 -0.563 0.003
19 0 0.06557377 -0.774 0.024
20 1 0.12565445 -0.475 0.012
21 1 1.235365854 0.799 8.733
22 0 0.5 0.699 0.7
23 0 0.400494438 -0.464 0.453
24 1 0.134407028 0.376 0
25 1 0.612575127 1.39 1.077
26 1 0.395833333 0.401 0.275
27 3 0.133540373 -0.506 0.019
28 4 0.423538831 0.74 0.289
29 0 0.056572923 -0.591 0
30 4 0.178217822 -0.007 0.019
31 0 0.014281464 -0.774 0
32 1 0.683944374 -0.122 1.443
33 3 0.242047026 -0.137 0.037
34 2 0.018329939 -0.774 0
35 0 0.01902369 -0.774 0
36 3 0.027950311 -0.774 0.001
37 2 0.102481122 -0.146 0
38 0 0.029216467 -0.774 0.001
39 2 0.075555556 -0.621 0.002
40 3 0.138416908 -0.315 0.012
41 4 0.012936295 -0.774 0
42 3 0.07192846 -0.62 0.001
43 2 0.776084408 0.357 1.576
44 1 0.307497894 -0.297 0.197
45 1 0.012658228 -0.774 0.031
46 2 0.087265918 -0.49 0.001
47 0 0.06959707 -0.774 0.06
48 3 0.915668663 1.868 1.81
49 3 0.12414966 -0.172 0
50 2 0.150568182 -0.029 0
51 2 0.629455279 1.27 0.89
52 1 0.185257032 -0.481 0.032
53 6 0.513695744 1.895 0.475
54 0 0.013129771 -0.774 0
55 4 0.424146427 1.15 0.005
56 5 1.180483592 2.572 1.595
57 0 0.060144346 -0.774 0.048
58 0 0.21628017 -0.116 0.089
59 0 0.949275362 0.249 3.099
60 4 0.262085308 1.206 0
61 0 0.009939898 -0.774 0
62 0 0.012658228 -0.774 0.031
63 0 0.517867959 0.517 0.468
64 0 0.355885079 -0.041 0.664
65 2 0.522111759 2.29 0.072
66 1 0.5 0.711 0.486
67 3 0.452774715 1.323 0.063
68 1 0.251425609 0.087 0.2
69 6 0.174879227 -0.127 0.083
70 3 0.618904726 1.051 1.137
71 3 0.498308906 1.657 0.313
72 0 0.016447368 -0.774 0
73 4 0.368305209 1.402 0.013
74 3 0.280938124 0.094 0.102
75 1 0.408256881 0.076 0.432
76 3 0.078081092 -0.205 0
77 5 0.95472232 2.606 0.052
78 2 0.295987888 -0.224 0.128
79 5 0.342105263 1.683 0.023
80 6 0.28725905 -0.04 0.227
81 2 0.274861878 0.322 0.08
82 3 0.19456617 -0.487 0.079
83 2 0.310836145 0.662 0.492
84 4 0.076431084 -0.209 0
85 5 0.056819768 0.012 0
86 2 0.05655058 0.518 0.106
87 7 0.024638457 -0.774 0.003
88 6 0.149277689 -0.1 0.004
89 3 0.089996414 -0.412 0
90 3 0.23802682 -0.127 0.161
91 4 0.319043693 -0.013 0.376
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93 3 0.084391337 -0.019 0
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95 6 0.048629769 -0.594 0
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97 0 0.603340292 -0.472 2.228
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99 1 0.320216049 -0.304 0.27
100 1 0.129179331 -0.774 0.398
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104 3 0.320325203 0.299 0.181
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106 1 0.273343766 -0.148 0.131
107 3 0.88841343 3.205 0.146
108 1 0.167713004 -0.481 0.044
109 0 0.030381383 -0.774 0.01
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113 0 0.038065028 -0.774 0.019
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115 6 0.21810567 0.652 0.003
116 3 0.345334882 0.246 0.037
117 0 0.036153846 -0.774 0.018
118 2 0.370267454 0.802 0.001
119 5 0.643486778 0.292 1.41
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148 4 0.016629712 -0.774 0
149 6 0.316793893 0.758 0.001
150 3 1.509191176 1.109 11.432
151 4 0.133737518 -0.196 0
152 3 0.096180396 -0.488 0.004
153 5 0.248 0.602 0.002
154 6 0.600923206 1.978 0.573
155 1 0.090523883 -0.181 0.002
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157 1 0.335315985 -0.296 0.319
158 1 0.118414322 -0.033 0.005
159 5 0.517106549 0.402 0.945
160 4 0.16211878 -0.774 0.16
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163 2 0.364935065 -0.5 0.311
164 0 0.171099007 -0.135 0.001
165 2 0.293103448 -0.489 0.128
166 0 0.102861562 -0.464 0.003
167 2 0.00618897 -0.774 0
168 1 0.016054228 -0.774 0
169 4 0.021779947 -0.774 0
170 0 0.064505879 -0.455 0.001
171 1 0.037588097 -0.774 0.019
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173 1 0.038301415 -0.774 0.004
174 4 0.413621852 0.751 0.109
175 1 0.022505878 -0.774 0.066
176 4 0.027683616 -0.774 0.004
177 3 0.128766741 0.646 0
178 2 0.023721666 -0.774 0
179 0 0.017982799 -0.774 0
180 4 0.328170029 1.031 0.003
181 7 0.704202232 2.115 0.091
182 4 0.394625177 1.66 0
183 4 0.461739455 2.347 0.144
184 0 0.216568047 -0.632 0.11
185 2 0.083552056 -0.605 0.018
186 5 0.554077253 1.79 0.71
187 0 0.171251109 -0.588 0.048
188 3 0.408383234 -0.194 0.489
189 0 0.075177305 -0.774 0.226
190 1 0.098947368 -0.605 0.034
191 0 0.019918699 -0.774 0
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194 0 0.027760252 -0.774 0.001
195 1 0.016612829 -0.774 0.001
196 2 0.069011379 -0.34 0
197 1 0.465510597 1.075 0.181
198 6 0.113065327 -0.36 0
199 0 0.050711744 -0.774 0.008
200 1 0.585513078 0.285 0.91
201 0 0.012658228 -0.774 0.031
202 0 0.050583658 -0.614 0.157
203 1 0.51372315 0.51 0.443
204 1 0.0625 -0.774 0.052
205 4 0.680672269 0.037 1.911
206 2 0.663917526 0.014 2.034
207 6 0.170434783 -0.563 0.167
208 2 0.039183673 -0.774 0.02
209 0 0.168615984 -0.456 0.098
210 1 0.10607169 -0.135 0.01
211 3 0.092382496 -0.487 0.001
212 5 0.02699784 -0.774 0.004
213 3 0.018613861 -0.774 0
214 3 0.493279022 0.823 0.38
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217 1 0.163166083 0.211 0
218 0 0.016208598 -0.774 0
219 3 0.387772194 0.307 0.138
220 6 0.813519814 1.374 3.867
221 5 0.007638889 -0.774 0
222 7 0.156528792 -0.591 0.148
223 1 0.141996558 -0.314 0.029
224 1 1.045517241 0.652 3.947
225 0 0.020096463 -0.774 0
226 0 0.027529496 -0.774 0
227 0 0.078171091 -0.774 0.062
228 3 0.02047667 -0.774 0
229 2 0.058426533 -0.433 0
230 5 0.013797241 -0.774 0
231 0 0.319974555 1.252 0.028
232 4 0.054144385 -0.63 0
233 3 0.191011236 -0.494 0.076
234 0 0.023225806 -0.774 0.006
235 1 0.012658228 -0.774 0.031
236 3 0.821643287 1.777 3.444
237 2 0.076215506 -0.624 0.002
238 1 0.015968772 -0.774 0
239 1 0.06266616 -0.621 0
240 0 0.028142589 -0.774 0.001
241 7 0.223042836 0.518 0.007
242 2 0.406481155 1.296 0.002
243 2 0.017844397 -0.774 0
244 2 0.310151878 1.103 0.005
245 0 0.282918149 -0.456 0.188
246 1 0.090839402 -0.256 0.001
247 0 0.021412472 -0.774 0
248 1 0.017016655 -0.774 0
249 4 0.307692308 -0.621 0.375
250 2 1.799363057 0.329 11.775
251 1 0.437054632 -0.335 0.528
252 3 0.228571429 0.594 0.017
253 0 0.079625293 -0.472 0
254 2 0.029535865 -0.774 0
255 1 0.177169607 -0.402 0.001
256 5 0.059423988 -0.62 0
257 2 0.249582638 -0.013 0.159
258 0 0.050761421 -0.774 0.009
259 1 0.046738072 -0.774 0.026
260 3 0.354354354 0.142 0.334
261 6 0.16497373 -0.22 0.008
262 0 0.022505878 -0.774 0.066
263 3 0.47696737 0.087 0.443
264 6 0.274623969 0.699 0.12
265 4 0.134405812 -0.473 0.028
266 0 0.012658228 -0.774 0.031
267 2 0.882352941 -0.619 3.721
268 5 0.146965977 -0.005 0
269 2 0.912912913 1.986 2.367
270 2 0.719314938 0.715 1.683
271 2 0.019847973 -0.774 0
272 4 0.074609821 -0.488 0.002
273 0 0.058823529 -0.774 0.006
274 1 0.70824295 0.19 1.194
275 1 0.166666667 -0.774 0.168
276 0 0.029722589 -0.774 0.001
277 0 0.018208844 -0.774 0
278 0 0.109555691 -0.476 0.038
279 3 0.018442623 -0.774 0
280 2 0.127659574 -0.774 0.072
281 0 0.028846154 -0.774 0.005
282 3 0.300250806 -0.05 0.001
283 5 0.626984127 -0.364 1.485
284 1 0.289664708 0.106 0
285 1 0.598159509 0.142 1.653
286 0 0.024440762 -0.774 0
287 1 0.098346388 -0.398 0.006
288 6 0.405913978 1.678 0.011
289 0 0.062268347 -0.513 0
290 0 0.130904184 -0.774 0.076
291 0 0.164021164 -0.368 0.113
292 6 0.316239316 0.643 0.03
293 1 0.085191956 -0.489 0.001
294 0 0.018525977 -0.774 0
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296 3 0.068546158 -0.295 0
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298 2 0.144851 -0.124 0.713
299 0 0.046833422 -0.476 0
300 4 0.37398374 0.858 0.11
301 6 0.4052311 1.4 0.005
302 4 0.936141759 3.942 0.107
303 5 0.978065022 2.146 0.844
304 1 0.006863073 -0.774 0
305 1 0.045172719 -0.774 0.026
306 0 0.018115942 -0.774 0
307 3 0.125066905 0.094 0
308 4 0.498047964 0.682 0.489
309 1 0.450067476 0.694 0.248
310 1 0.043046358 -0.774 0.002
311 2 0.331718438 1.427 0
312 1 1.26417704 0.556 7.344
313 1 0.023234201 -0.774 0.001
314 0 1.067000385 4.642 0.565
315 2 0.028558268 -0.774 0.001
316 0 0.174981104 0.789 0
317 1 0.086500655 -0.464 0
318 2 0.049226885 -0.502 0
319 3 0.158812441 -0.402 0.075
320 0 0.007956052 -0.774 0
321 1 0.034790366 -0.774 0.001
322 0 0.017450683 -0.774 0
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325 0 0.262056415 -0.349 0.378
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328 2 0.069124424 -0.774 0.026
329 6 0.138632163 -0.163 0
330 4 0.043983402 -0.774 0.026
331 1 0.052045177 -0.366 0
332 6 0.040925267 -0.774 0.004
333 3 0.029748993 -0.632 0
334 5 0.312984496 -0.456 0.218
335 3 0.014367816 -0.774 0
336 3 0.063161876 -0.642 0
337 1 0.072547403 -0.64 0.001
338 2 0.142857143 -0.503 0.024
339 2 0.028149191 -0.774 0
340 4 0.136517329 -0.305 0.012
341 2 0.52775543 1.659 0.316
342 6 0.564784053 3.142 0.001
343 3 0.562111801 0.757 0.996
344 4 0.239656518 -0.508 0.055
345 6 0.760460251 0.198 1.785
346 0 0.035344302 -0.774 0.001
347 6 0.012658228 -0.774 0.031
348 5 0.187602852 -0.307 0.049
349 6 0.056841389 -0.511 0
350 5 0.510376959 1.233 0.574
351 3 0.355704698 -0.572 1.18
352 2 0.719921105 0.35 2.384
353 1 0.172888016 -0.157 0.023
354 3 0.155591572 -0.09 0.201
355 0 0.164965986 -0.589 0.16
356 0 0.064587156 -0.585 0
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358 0 0.024851432 -0.774 0.003
359 3 0.023838882 -0.774 0
360 1 0.154462243 -0.424 0.025
361 1 0.458811262 -0.28 0.502
362 0 0.02027027 -0.774 0
363 2 0.01969697 -0.774 0
364 2 0.015441631 -0.774 0
365 0 0.014990631 -0.774 0
366 6 0.017090909 -0.774 0
367 1 0.305263158 -0.774 0.913
368 2 0.060563871 -0.482 0
369 3 0.168037782 0.626 0
370 3 0.748409485 1.715 0.092
371 1 0.362424242 1.331 0
372 5 0.318941504 1.188 0.027
373 4 0.060469589 2.795 0.001
374 0 0.221729062 1.264 0
375 1 0.479022255 0.841 0.058
376 1 0.570394737 1.324 0.005
377 0 0.033376304 1.085 0
378 1 0.410115783 2.015 0
379 0 0.084647739 0.068 0

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