GENE
stringlengths
1
15
WT_1
float64
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78
LKB1_KO
float64
-52.01
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PTEN_KO
float64
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78
VHL_KO
float64
-52.01
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WT_2
float64
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78
CDH1_KO
float64
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NF2_KO
float64
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BAP1_KO
float64
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WT_3
float64
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ARID1A_KD
float64
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PBRM1_KO
float64
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WT_4
float64
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KEAP1_KO
float64
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NF1_KO
float64
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RB1_KO
float64
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TP53_KO
float64
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TP53BP1_KO
float64
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A1BG
-2.71
-0.141
-2.97
-15.637
2.833
-5.615
-16.178
-2.007
-8.348
-7.767
-3.43
-0.122
4.157
-3.21
1.068
-3.176
-14.87
A1CF
0.487
4.652
-0.177
13.089
1.4
2.038
-9.4
-1.94
6.171
2.121
0.35
6.466
-5.686
3.56
1.092
-1.683
3.698
A2M
10.155
16.736
1.193
16.533
3.841
2.673
-5.46
9.253
5.307
6.289
-0.172
-4.5
15.884
-1.057
11.155
13.842
0.112
A2ML1
-8.586
-7.187
-14.078
-12.774
-11.808
-9.192
-16.024
-18.318
-0.419
-9.831
-11.444
-4.428
-5.983
-8.374
-6.805
-16.286
-4.478
A3GALT2
-6.135
-4.118
-2.868
-4.555
-7.567
-2.208
-11.901
-3.046
-8.586
-5.159
-7.293
-6.957
-12.695
-9.676
-14.437
-12.219
-4.792
A4GALT
-7.356
-12.879
-7.509
-18.747
-12.461
-7.089
-17.766
-10.367
-7.866
-1.409
-7.975
-4.663
-12.291
-3.696
-6.19
-14.889
-8.022
A4GNT
-11.987
-10.938
-11.877
-9.612
-14.376
-16.705
-8.848
-9.492
-13.893
-13.317
-14.872
-10.635
-12.836
-12.298
-9.096
-8.472
-5.256
AAAS
-1.83
-9.091
-4.816
-8.041
1.833
3.59
-17.341
-14.279
9.997
-0.248
-12.44
-14.097
-1.46
2.024
-1.901
8.926
-0.577
AACS
-15.021
-8.9
-14.464
-17.322
-10.368
-8.115
-4.995
-7.037
-12.512
-13.196
-19.127
-2.889
-11.482
-17.717
-10.318
-4.933
-15.673
AADAC
-21.239
-24.46
-22.065
-14.884
-21.154
-19.802
-16.413
-21.372
-23.691
-25.554
-16.858
-21.447
-24.938
-18.146
-13.353
-15.292
-18.714
AADACL2
-13.924
-14.835
-20.54
-22.896
-11.985
-12.648
-17.125
-15.419
-12.138
-16.279
-16.153
-12.618
-11.999
-14.29
-22.283
-14.987
-11.908
AADACL3
-12.063
-9.66
-16.644
-5.17
-14.516
-15.066
-10.628
-15.404
-8.908
-8.106
-8.542
-13.231
-11.186
-4.774
-14.926
-9.832
-18.796
AADACL4
-6.454
-16.478
-6.905
-15.506
-9.675
-5.922
-7.294
-11.33
-5.905
-9.673
-3.088
-17.709
-16.72
-4.133
-13.442
-3.817
-15.827
AADAT
-24.942
-18.815
-21.986
-26.266
-23.037
-22.088
-21.289
-21.132
-25.881
-21.155
-25.422
-22.793
-20.241
-15.529
-22.588
-27.044
-24.736
AAED1
-11.308
-6.352
-10.402
-4.488
-12.436
-7.631
-11.243
-7.579
-16.069
-17.889
-12.554
-16.854
-14.117
-16.454
-17.644
-17.476
-11.43
AAGAB
-10.377
-7.757
-18.191
-7.545
-9.689
-6.918
-10.247
-8.499
-10.573
-13.37
-19.937
-9.252
-13.713
-11.655
-11.775
-9.894
-22.524
AAK1
-10.14
-15.939
-13.267
-7.415
-11.323
-2.809
-15.941
-14.93
-14.227
-9.522
-7.373
-12.106
-18.963
-17.6
-17.679
-14.889
-19.08
AAMDC
-16.261
-17.124
-20.311
-21.801
-12.048
-19.301
-25.333
-20.826
-18.998
-15.952
-14.011
-13.543
-11.332
-21.28
-6.042
-16.726
-10.178
AAMP
29.135
31.172
33.879
24.962
20.278
23.401
18.276
22.009
29.992
24.13
25.717
27.846
22.545
17.436
34.389
17.947
15.803
AANAT
-14.134
-24.722
-31.073
-21.249
-29.007
-24.172
-14.658
-23.508
-18.265
-21.379
-24.268
-32.887
-27.926
-14.953
-20.808
-15.504
-23.968
AAR2
-7.112
-4.011
-24.775
11.62
-6.744
-10.906
-9.909
-14.428
-9.551
-13.896
-4.028
-6.298
-15.8
-0.816
-22.348
-8.787
-2.658
AARD
-4.795
-9.094
-6.568
-9.428
-6.681
-9.787
-5.347
-5.852
-9.538
-6.957
-15.977
-7.648
-15.656
-1.964
-13.548
-7.087
-5.428
AARS
43.42
40.258
36.581
42.392
27.621
33.907
28.937
31.864
38.65
42.925
38.829
37.576
41.809
42.227
47.886
39.802
39.276
AARS2
-16.216
-18.241
-13.468
-5.993
-14.268
-15.458
-12.163
-16.757
-24.745
-3.296
-7.831
-18.14
-18.174
-13.163
-13.273
-27.217
-17.401
AARSD1
-1.888
-0.514
-1.772
-5.893
0.56
-2.112
-3.63
-2.397
-1.61
-0.987
1.131
-2.374
-3.11
-6.211
3.632
-2.77
-2.164
AASDH
-21.404
-17.458
-15.681
-22.913
-22.312
-18.746
-13.629
-19.533
-21.248
-21.149
-13.711
-12.295
-14.686
-17.21
-7.128
-11.28
-20.018
AASDHPPT
29.028
29.319
18.331
17.776
24.774
12.343
17.149
16.97
22.477
27.155
19.378
12.54
15.751
22.401
8.748
28.431
30.942
AASS
-22.873
-19.33
-16.654
-9.468
-21.581
-20.98
-19.405
-17.362
-17.966
-19.258
-21.106
-18.13
-22.367
-9.109
-16.826
-16.042
-23.404
AATF
13.842
2.673
19.966
2.783
14.457
1.606
7.079
19.187
14.994
12.999
2.673
27.392
9.865
12.21
21.394
26.85
25.776
AATK
-9.357
-2.157
-2.215
-7.576
-7.1
-0.59
-1.345
-11.118
-2.975
-2.347
-3.662
1.257
11.307
3.712
7.523
2.992
-8.236
ABAT
-10.114
-15.883
-13.629
-16.837
-15.668
-17.957
-13.464
-12.156
-16.402
-18.632
-12.855
-20.124
-23.566
-11.319
-18.195
-11.599
-11.969
ABCA1
-12.249
-13.355
-18.622
-10.598
-18.504
-13.045
-16.28
-16.647
-10.283
-20.352
-14.559
-23.144
-18.924
-10.607
-17.59
-18.38
-10.382
ABCA10
-11.146
-18.28
-20.155
-20.107
-26.191
-26.123
-17.097
-21.39
-19.378
-16.645
-21.316
-23.534
-15.249
-16.339
-17.402
-14.947
-16.183
ABCA12
-20.079
-15.472
-23.262
-12.33
-18.33
-22.929
-18.778
-20.335
-21.486
-20.335
-24.983
-25.295
-23.198
-15.909
-15.996
-13.529
-18.778
ABCA13
-22.49
-22.824
-21.688
-17.66
-28.16
-24.519
-12.64
-22.775
-25.115
-21.822
-17.137
-16.132
-23.147
-18.466
-25.958
-29.021
-17.946
ABCA2
1.334
4.982
0.534
-1.765
11.289
3.196
1.097
-3.592
-0.305
-0.282
3.247
4.03
11.586
7.767
8.885
16.036
-3.882
ABCA3
-5.893
-8.369
-7.474
-7.374
-6.19
-5.345
-11.5
-9.757
0.288
-1.571
-8.592
-12.905
-14.926
-7.934
-11.715
-10.377
-14.14
ABCA4
-11.636
-28.027
-17.898
-17.207
-21.447
-6.653
-16.901
-16.037
-13.601
-14.071
-15.826
-17.591
-17.735
-17.142
-17.558
-23.537
-6.32
ABCA5
-23.947
-24.899
-23.949
-26.81
-28.806
-28.793
-14.26
-26.381
-22.915
-20.573
-27.131
-21.253
-30.757
-6.736
-10.7
-24.8
-12.846
ABCA6
-31.132
-17.488
-16.924
-23.332
-22.047
-25.059
-17.931
-24.079
-17.494
-24.318
-16.386
-21.596
-21.624
-21.836
-28.223
-17.686
-22.472
ABCA7
-11.838
-21.441
-0.33
-12.687
-13.043
-8.437
-17.846
-6.94
-16.733
-11.46
-9.042
-1.662
-6.529
-20.84
-6.883
-16.131
-4.464
ABCA8
-12.091
-21.509
-10.23
-7.603
-22.053
-16.845
-13.453
-15.514
-15.011
-17.397
-11.125
-4.795
-9.966
-6.154
-21.665
-14.532
-16.253
ABCA9
-16.455
-22.19
-9.742
-17.413
-19.611
-23.575
-23.164
-13.813
-17.907
-21.97
-13.402
-17.535
-11.098
-12.342
-19.985
-6.502
-19.975
ABCB1
-16.103
-15.11
-16.385
-23.396
-16.444
-15.14
-22.655
-16.092
-21.251
-19.162
-15.95
-17.82
-20.025
-21.245
-20.724
-24.348
-19.512
ABCB10
-2.028
-8.266
-7.534
-5.826
-5.466
-8.617
-6.136
-3.478
-5.819
-6.936
-6.927
3.027
-7.272
-11.49
1.761
-4.321
-1.78
ABCB11
-18.792
-15.102
-17.075
-13.24
-25.734
-12.279
-17.792
-15.016
-22.413
-14.998
-17.832
-16.494
-17.31
-17.587
-16.583
-13.485
-15.483
ABCB4
-19.761
-12.965
-13.408
-16.642
-16.426
-14.819
-14.669
-16.753
-14.405
-13.402
-12.008
-18.291
-11.577
-18.257
-15.505
-15.025
-16.083
ABCB5
-20.621
-20.926
-13.651
-15.563
-19.915
-12.512
-18.823
-12.452
-16.162
-15.652
-16.697
-13.599
-24.22
-21.896
-19.087
-25.372
-11.626
ABCB6
-17.276
-13.104
-21.04
-15.463
-17.187
-10.246
-21.024
-16.448
-16.641
-22.312
-10.055
-9.711
-13.105
-19.484
-14.623
-23.622
-19.168
ABCB7
9.455
7.896
-0.545
-3.977
8.215
2.109
7.781
9.358
6.233
8.04
-2.495
13.182
-3.705
-0.624
3.968
-7.48
13.089
ABCB8
-11.393
-10.304
-9.524
-23.048
-2.991
-14.178
-11.781
-1.428
-10.384
-8.089
-14.475
-21.233
-13.87
-17.473
-4.468
-7.883
-20.536
ABCB9
-8.254
-12.25
-5.696
-7.22
-10.024
-1.537
-14.845
-12.534
-6.927
-3.072
-6.231
-1.521
0.838
-7.747
-2.069
-6.138
-6.046
ABCC1
-19.187
-23.406
-21.903
-21.148
-18.272
-20.142
-20.304
-15.959
-23.797
-21.48
-16.994
-18.577
-17.871
-9.959
-25.176
-19.209
-16.742
ABCC10
-16.398
-10.163
-13.58
-17.079
-12.282
-10.529
-11.481
-10.848
-10.397
-17.257
-19.658
-1.261
-9.55
-11.84
-10.956
-9.798
-20.419
ABCC11
-14.319
-18.064
-28.71
-15.952
-12.12
-21.337
-18.116
-9.427
-25.056
-19.004
-24.06
-14.087
-20.155
-25.062
-16.56
-19.128
-20.956
ABCC12
-18.709
-18.029
-21.97
-9.119
-18.203
-17.695
-22.629
-15.95
-16.339
-14.061
-15.378
-19.01
-10.808
-17.994
-7.517
-14.854
-15.977
ABCC2
-14.02
-10.848
-14.185
-4.82
-17.515
-14.759
-11.409
-16.019
-12.651
-8.453
-7.394
-16.944
-15.53
-25.252
-16.526
-12.83
-15.29
ABCC3
-13.407
-13.941
-5.769
-8.326
-6.943
-8.458
-14.754
-12.324
-12.812
-8.314
-3.096
-1.856
9.93
6.663
-9.29
-3.962
-15.688
ABCC4
-24.036
-25.695
-27.34
-23.425
-21.378
-26.439
-20.694
-22.005
-26.102
-24.36
-26.23
-16.271
-25.162
-14.722
-26.462
-25.039
-19.857
ABCC5
-20.402
-17.322
-15.805
-29.997
-11.06
-18.536
-17.024
-16.008
-18.238
-17.226
-13.646
-15.578
-14.709
-12.156
-16.582
-16.632
-16.774
ABCC6
5.053
15.059
12.95
25.799
8.625
14.283
6.321
26.304
15.717
6.909
10.684
9.22
10.215
17.19
11.527
18.882
11.771
ABCC8
-15.259
-16.828
-11.724
-14.512
-22.176
-18.35
-11.883
-16.552
-11.711
-22.931
-13.032
-13.053
-15.438
-16.161
-15.031
-14.575
-20.66
ABCC9
-18.038
-14.878
-17.109
-13.127
-13.163
-18.028
-17.2
-19.225
-20.853
-17.528
-24.229
-18.101
-21.784
-18.502
-25.433
-24.033
-14.082
ABCD1
-9.24
-3.197
-9.142
-15.738
-5.041
-10.429
-3.814
-16.592
-6.591
-14.096
-15.09
-2.171
-13.472
-12.063
-8.968
2.666
-16.147
ABCD2
-17.395
-17.949
-22.507
-18.4
-20.544
-14.987
-22.903
-18.373
-17.538
-19.212
-24.87
-19.548
-21.441
-20.098
-19.912
-22.991
-17.421
ABCD3
-2.603
-18.987
-3.37
-7.968
-10.542
-4.761
-1.495
-9.793
-2.478
-3.019
-10.522
-3.648
-6.464
-0.73
1.446
-10.85
5.274
ABCD4
-12.116
-9.94
-12.037
-18.368
-15.793
-8.124
-13.258
-13.435
-10.431
-13.564
-13.176
-10.746
-22.546
-2.523
-7.066
-10.573
-17.021
ABCE1
37.062
38.577
30.39
34.263
47.277
55.618
30.809
29.67
38.577
41.605
49.595
17.207
26.367
33.066
10.578
15.267
9.058
ABCF1
10.624
-2.622
19.846
10.744
12.54
8.734
11.307
3.546
12
0.012
16.781
37.266
9.93
20.837
16.906
21.279
24.095
ABCF2
-11.708
-18.466
-19.566
-14.882
-20.537
-15.064
-22.386
-9.907
-13.984
-15.768
-11.646
-24.86
-8.039
-13.231
-11.478
-0.811
-17.344
ABCF3
-19.238
-14.956
-15.216
-18.157
-16.594
-21.262
-16.42
-18.977
-16.659
-17.222
-17.173
-11.352
-15.16
-16.551
-17.411
-18.824
-19.466
ABCG1
-24.862
-22.513
-18.577
-21.246
-17.797
-16.398
-24.278
-13.65
-16.823
-16.73
-20.194
-18.537
-24.149
-19.462
-13.79
-26.385
-14.082
ABCG2
-27.861
-29.528
-19.941
-27.276
-25.545
-29.265
-24.018
-25.804
-21.799
-30.307
-20.286
-13.428
-21.968
-19.904
-35.335
-20.838
-20.116
ABCG4
-22.83
-22.606
-24.538
-16.014
-19.396
-19.319
-16.575
-19.012
-17.96
-27.955
-20.926
-29.449
-20.582
-19.574
-17.636
-18.979
-21.057
ABCG5
-20.221
-11.767
-24.97
-7.152
-18.402
-13.828
-25.94
-24.658
-14.108
-12.069
-16.934
-18.371
-18.307
-15.197
-15.515
-19.338
-15.657
ABCG8
-14.346
-5.303
-17.792
-16.402
-16.401
-15.559
-14.353
-15.944
-12.214
-14.885
-12.543
-14.994
-10.836
-24.137
-23.676
-13.123
-21.774
ABHD1
-18.658
-16.594
-12.338
-12.504
-17.047
-13.976
-9.285
-10.079
-21.334
-10.323
-17.097
-24.001
-16.667
-4.274
-18.973
-17.175
-23.139
ABHD10
-15.188
-15.225
-10.655
-15.36
-18.574
-13.897
-13.848
-13.802
-14.47
-13.167
-13.806
-13.516
-13.897
3.196
-11.867
-25.389
-11.313
ABHD11
7.587
-4.118
2.949
8.08
5.911
8.97
12.058
19.966
-1.347
-2.991
4.516
4.564
5.243
24.989
6.575
-3.085
-3.146
ABHD12
-22.773
-21.948
-29.564
-22.243
-21.453
-27.029
-28.369
-16.655
-26.983
-26.092
-21.201
-20.036
-30.394
-21.13
-21.324
-26.207
-20.84
ABHD12B
-13.114
-16.82
-17.57
-18.141
-16.295
-9.545
-14.082
-17.171
-12.66
-7.859
-10.024
-10.444
-11.603
-11.578
-13.373
-15.4
-9.387
ABHD13
-18.228
-29.7
-21.788
-18.651
-21.523
-24.506
-26.764
-24.636
-21.125
-29.449
-21.733
-19.012
-26.228
-4.267
-14.92
-19.066
-18.104
ABHD14A
-8.767
-6.945
-10.651
-5.767
-11.279
-9.914
-10.542
-11.395
-7.181
-10.663
-17.113
-3.13
-6.482
-13.953
-6.057
-3.705
-16.041
ABHD14B
-17.864
-0.955
-3.1
-3.578
-10.407
-16.062
1.384
-7.947
-9.14
-1.239
-12.012
-9.02
-1.14
-15.415
-10.241
-2.688
-18.398
ABHD15
-10.961
-22.206
-14.288
-13.099
-12.942
-17.661
-11.999
-19.892
-12.271
-9.452
-11.082
-14.224
-8.89
-13.602
-9.648
-3.191
-14.113
ABHD16A
-10.388
1.29
-10.64
-9.128
-5.368
-1.981
-10.071
1.179
-8.643
-6.666
-1.6
-7.25
-2.588
-14.319
-0.012
-11.38
-15.407
ABHD16B
-8.762
-8.91
-9.279
4.612
-12.882
-17.062
-11.61
-12.61
-15.611
-15.203
-4.836
-10.635
-18.848
-11.077
-13.001
-11.06
-8.963
ABHD17A
5.679
6.663
3.722
-13.72
11.742
-0.769
1.352
13.952
9.722
3.418
13.318
7.414
21.212
14.226
9.34
8.354
0.107
ABHD17B
-20.425
-17.684
-16.582
-19.697
-23.41
-13.127
-12.797
-19.897
-28.33
-26.566
-21.033
-22.706
-16.433
-25.658
-22.936
-22.319
-16.313
ABHD17C
-21.501
-17.116
-20.573
-17.44
-22.755
-23.12
-12.689
-17.21
-14.948
-15.08
-23.21
-29.346
-23.464
-14.188
-15.253
-13.189
-14.868
ABHD2
-18.305
-30.287
-20.164
-21.702
-22.58
-21.696
-18.336
-23.213
-23.512
-23.243
-22.47
-25.549
-26.507
-21.506
-28.036
-25.222
-23.332
ABHD3
-13.849
-1.063
-8.212
-6.574
-7.776
-0.554
-8.83
-5.764
-6.428
-5.203
-5.698
-14.856
-5.447
-17.379
-6.081
4.96
-1.653
ABHD4
-26.869
-24.963
-21.927
-23.937
-20.729
-19.654
-21.35
-20.207
-27.022
-27.441
-21.064
-25.341
-13.376
-18.333
-25.654
-17.563
-20.212
ABHD5
-10.74
-17.079
-18.237
-14.969
-14.312
-16.138
-9.778
-17.415
-15.911
-22.158
-17.077
-20.383
-17.987
-24.072
-9.139
-14.963
-12.725
ABHD6
-20.59
-15.958
-13.531
-12.324
-10.689
-14.798
-18.747
-13.407
-15.682
-7.846
-18.679
-5.751
-11.449
-2.535
-3.919
-8.878
-7.956
ABHD8
-14.119
-7.668
-13.028
-18.582
-16.511
-15.558
-16.905
-7.367
-19.765
-12.774
-12.204
-16.665
-12.733
-14.088
-12.875
-8.893
-15.224
ABI1
-2.335
-2.326
-6.052
-1.47
-4.173
-4.778
-2.397
-6.736
-6.852
-2.722
-4.366
-10.686
-13.368
-7.293
-7.374
-9.555
0.1
ABI2
-20.435
-18.103
-23.1
-18.517
-19.088
-18.904
-20.088
-18.092
-23.376
-24.993
-23.671
-24.938
-15.874
-21.161
-20.042
-18.775
-22.868
ABI3
-12.725
-13.978
-10.989
-13.145
-11.064
-12.023
-8.748
-14.109
-13.513
-5.967
-7.424
-4.381
-14.834
-7.438
-9.848
-15.066
-10.134
ABI3BP
-22.252
-18.97
-18.568
-20.955
-18.552
-26.102
-19.001
-17.137
-21.96
-25.195
-19.581
-27.072
-18.461
-15.007
-20.29
-21.679
-12.515

Dataset Card for PMC_35559673_table_s datasets

Dataset Details

Dataset Description

This dataset contains the results of genome-wide CRISPR screens using isogenic knockout cells to uncover vulnerabilities in tumor suppressor-deficient cancer cells. The data were originally published by Feng et al., Sci. Adv. 8, eabm6638 (2022), and are available via PubMed Central (PMC). The supplementary tables included in this dataset provide detailed data on raw counts, essentiality calls, Bayes factors, and synthetic lethality (SL) hits. The dataset supports research into genetic dependencies and potential therapeutic targets.

  • Curated by: Feng et al., Sci. Adv. 8, eabm6638 (2022)
  • Funded by: Likely supported by institutions affiliated with the authors.
  • Shared by: Feng et al.
  • Language(s): Not applicable (biomedical dataset).
  • License: CC BY 4.0

Dataset Sources

Dataset Structure

This dataset consists of seven tables (S1-S7), each representing a different aspect of the CRISPR screen results:

  1. Table S1: Raw counts for all CRISPR screens in this study.

    • File Mapping: sciadv.abm6638_table_s1.xlsx
  2. Table S2: Binary essentiality calls matrix.

    • File Mapping: sciadv.abm6638_table_s2.xlsx
  3. Table S3: Quantile-normalized Bayes factor (QBF) matrix.

    • File Mapping: sciadv.abm6638_table_s3.xlsx
  4. Table S5: Total SL hits identified for each TSG KO screen.

    • File Mapping: sciadv.abm6638_table_s5.xlsx
  5. Table S6: Shared SL hits across each TSG KO screen.

    • File Mapping: sciadv.abm6638_table_s6.xlsx
  6. Table S7: Unique SL hits for each TSG KO screen.

    • File Mapping: sciadv.abm6638_table_s7.xlsx

Dataset Creation

Curation Rationale

This dataset was curated to facilitate research into the vulnerabilities of cancer cells deficient in tumor suppressor genes. The binary essentiality calls, synthetic lethality (SL) hits, and other data allow researchers to explore genetic interactions that could serve as potential therapeutic targets. The methodology behind the CRISPR screens and SL hit identification was detailed by Feng et al. in their 2022 study.

Data Collection and Processing

Data were collected from genome-wide CRISPR screens performed on isogenic knockout cells. The data were processed to produce raw counts, binary essentiality calls, and genetic interaction matrices, including shared and unique synthetic lethal hits.

Relevant references describing the data processing and methods can be found in the following sources:

  • Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens (PMID: 28655737)
  • High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities (PMID: 26627737)
  • Identifying chemogenetic interactions from CRISPR screens with drugZ (PMID: 31439014)

Who are the source data producers?

The data were produced by Feng et al., as part of their research published in Science Advances. The researchers were affiliated with academic institutions engaged in cancer genomics and CRISPR screening methodologies.

Annotations

Annotation Process

Annotations were primarily focused on identifying shared and unique synthetic lethality hits across tumor suppressor knockout screens. Automated processing tools like CRISPR analysis pipelines were employed for initial hit identification, followed by manual validation based on genetic interactions.

Who are the annotators?

The original authors, including experts in CRISPR screening and cancer genomics, performed the annotations. No third-party annotations were added.

Bias, Risks, and Limitations

The dataset is limited to specific cancer cell lines and tumor suppressor gene knockouts. As a result, the findings may not be generalizable across all cancer types. Users should exercise caution when interpreting results outside the experimental context.

Recommendations

Users should consult the references provided to better understand the experimental design and limitations. The dataset is best suited for research applications in cancer genomics, genetic interactions, and therapeutic target discovery.

Citation

BibTeX:

@article{
  doi:10.1126/sciadv.abm6638,
  author = {Xu Feng  and Mengfan Tang  and Merve Dede  and Dan Su  and Guangsheng Pei  and Dadi Jiang  and Chao Wang  and Zhen Chen  and Mi Li  and Litong Nie  and Yun Xiong  and Siting Li  and Jeong-Min Park  and Huimin Zhang  and Min Huang  and Klaudia Szymonowicz  and Zhongming Zhao  and Traver Hart  and Junjie Chen },
  title = {Genome-wide CRISPR screens using isogenic cells reveal vulnerabilities conferred by loss of tumor suppressors},
  journal = {Science Advances},
  volume = {8},
  number = {19},
  pages = {eabm6638},
  year = {2022},
  doi = {10.1126/sciadv.abm6638},
  URL = {https://www.science.org/doi/abs/10.1126/sciadv.abm6638},
  eprint = {https://www.science.org/doi/pdf/10.1126/sciadv.abm6638},
  abstract = {Exploiting cancer vulnerabilities is critical for the discovery of anticancer drugs. However, tumor suppressors cannot be directly targeted because of their loss of function. To uncover specific vulnerabilities for cells with deficiency in any given tumor suppressor(s), we performed genome-scale CRISPR loss-of-function screens using a panel of isogenic knockout cells we generated for 12 common tumor suppressors. Here, we provide a comprehensive and comparative dataset for genetic interactions between the whole-genome protein-coding genes and a panel of tumor suppressor genes, which allows us to uncover known and new high-confidence synthetic lethal interactions. Mining this dataset, we uncover essential paralog gene pairs, which could be a common mechanism for interpreting synthetic lethality. Moreover, we propose that some tumor suppressors could be targeted to suppress proliferation of cells with deficiency in other tumor suppressors. This dataset provides valuable information that can be further exploited for targeted cancer therapy. Whole-genome CRISPR screens uncover synthetic lethal interactions for tumor suppressors.}
}

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