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Status
Public on Jan 17, 2007
Title
Identification of novel functional TBP-binding sites and general factor repertoires
Organism
Homo sapiens
Experiment type
Genome binding/occupancy profiling by array
Summary
We performed a comprehensive ChIP-on-chip analysis for 28 transcription factors on a large set of known and novel TBP binding sites experimentally identified via ChIP-cloning. A large fraction of identified TBP binding sites is located in introns or lacks a gene/mRNA annotation and found to direct transcription. Distinct profiles for general transcription factors and TAF-containing complexes were uncovered for RNAP II promoters located in CpG- and non-CpG islands suggesting distinct transcription initiation pathways. Keywords: TBP, Promoter, ChIP-on-chip, transcription factor profiling
Overall design
DNA fragments from ChIP with TBP antibodies and human U2OS cells were cloned, amplified and printed on glass slides to obtain TBP-binding sites microarray. ChIP has been performed with 28 antibodies against transcripton factors and histone marks, DNA from ChIP and input was amplified and hybridyzed on the TBP-binding sites microarray. The median ChIP/input ratios were normalized to median value of negative controls (myoglobin exons and promoter), averaged between 2 hybridizations and calculated as log2. For correlation analysis those targets with TBP ratio >2 were selected. Additionally, these targets were split to 2 datasets which contain targets overlapped and non-ovelapped with CpG islands (alignment and definition of UCSC genome browser).
Citation(s)
17268553
Submission date
Jan 12, 2007
Last update date
Mar 16, 2012
Contact name
S Denissov
Organization name
NCMLS
Street address
Geert Grooteplein 26
City
Nijmegen
ZIP/Postal code
6525 GA
Country
Netherlands
Platforms (1)
GPL4665
NCMLS Homo sapiens 1.3K TBP ChIP-cloning array
Samples (28)
Relations
BioProject
PRJNA98973
Table 1: Targets that overlap with CpG islands header descriptions
ID_REF
CpG TFIIB
CpG TFIIEa
CpG RNAPIICTD
CpG NC2a
CpG TAF1
CpG TAF4
CpG TAF7
CpG TAF12
CpG TAF10
CpG CBP_p300
CpG TRRAP
CpG PCAF
CpG SNAP19
CpG SNAP43
CpG SNAP45
CpG SNAP50
CpG SNAP190
CpG Bdp1
CpG Brf1
CpG RNAPIII
CpG UBF
CpG RPA116
CpG PAF53
Data table
ID_REF
CpG TFIIB
CpG TFIIEa
CpG RNAPIICTD
CpG NC2a
CpG TAF1
CpG TAF4
CpG TAF7
CpG TAF12
CpG TAF10
CpG CBP_p300
CpG TRRAP
CpG PCAF
CpG SNAP19
CpG SNAP43
CpG SNAP45
CpG SNAP50
CpG SNAP190
CpG Bdp1
CpG Brf1
CpG RNAPIII
CpG UBF
CpG RPA116
CpG PAF53
A10-5-39_
4.169
2.35
1.618
2.87
1.56
0.797
-0.457
1.199
2.021
1.967
2.403
2.161
2.175
0.802
0.218
0.003
1.567
0.466
3.201
3.611
3.319
1.952
2.625
A11-10-46_
3.671
0.819
1.026
1.739
1.34
1.242
0.606
1.769
1.359
2.099
1.324
1.581
1.607
0.364
0.681
0.063
1.044
0.991
2.829
2.562
2.982
1.092
1.904
A3-1-39_
3.437
1.316
1.316
1.632
1.371
0.975
0.792
1.787
3.667
2.231
1.633
2.208
3.384
0.807
1.208
-0.112
1.186
0.837
2.379
2.928
3.033
0.743
1.753
A3-4-46_
3.848
1.089
1.225
1.477
1.526
0.468
0.152
0.436
2.844
0.311
2.236
2.443
2.714
-0.013
0.813
0.172
1.178
0.981
3.101
3.684
3.518
0.721
1.758
A4-10-39_
4.09
1.151
1.025
1.717
1.527
0.722
1.49
0.982
0.981
2.065
1.449
1.449
1.207
0.572
1.512
0.218
1.026
1.076
3.204
3.409
3.15
1.51
1.86
A6-9-46_
3.993
2.061
1.404
0.593
1.808
0.434
0.529
1.54
1.759
2.726
1.87
1.98
1.304
1.178
1.282
0.031
1.074
0.709
3.158
3.832
3.425
0.563
1.409
A9-8-39_
4.138
0.968
1.355
0.779
2.291
0.953
0.914
0.608
0.735
1.635
2.346
2.083
2.446
0.019
0.612
0.424
1.371
1.127
3.188
3.67
3.862
0.045
2.302
B12-9-46_
4.631
0.911
1.832
0.898
2.004
1.39
0.719
1.533
1.236
1.915
2.761
2.798
3.094
-0.133
0.333
0.162
1.595
1.548
3.01
3.705
3.31
0.35
2.575
B3-8-39_
3.228
1.147
1.09
1.177
1.142
0.378
-0.539
0.824
2.998
0.821
0.955
1.044
1.3
0.81
1.491
0.056
0.693
0.599
2.112
2.614
2.678
0.974
1.388
B5-9-46_
4.082
2.005
1.036
0.906
1.384
0.391
1.179
0.18
2.011
1.506
2.14
1.204
2.388
0.437
-0.002
-0.173
1.156
0.62
2.883
3.13
3.035
0.372
0.932
B6-3-46_
4.088
0.785
1.252
0.781
2.061
1.316
0.334
1.078
1.199
1.936
2.099
1.41
1.846
0.056
0.405
-0.077
1.197
0.87
3.2
3.521
3.45
0.324
2.559
B8-2-46_
2.795
1.85
1.49
2.546
1.471
0.593
-0.563
-0.235
2.134
1.185
1.914
2.251
3.217
1.566
2.343
0.692
2.71
2.385
0.676
0.022
2.354
0.938
1.029
B9-9-46_
3.944
1.324
1.709
1.227
2.224
1.245
2.078
2.135
2.355
3.345
2.019
2.577
2.035
1.505
2.087
-0.05
1.622
1.281
3.014
3.69
3.307
0.553
1.907
C4-3-46_
3.973
1.743
1.165
0.761
1.807
0.219
-0.039
-0.063
1.014
0.667
2.036
2.19
1.263
0.496
0.293
-0.285
1.306
0.387
3.127
3.541
3.443
0.759
1.83
C4-8-39_
4.051
1.848
1.386
1.137
1.552
0.473
0.478
0.38
1.244
1.664
1.766
1.709
1.303
0.869
0.785
-0.449
1.422
0.583
3.31
3.897
3.385
1.066
2.21
C6-4-46_
3.618
1.308
1.17
1.141
1.356
0.377
0.061
0.486
2.024
0.326
1.758
1.956
1.939
0.061
0.939
0.228
1.036
0.863
2.678
3.291
3.349
0.784
1.685
C7-2-46_
4.005
1.666
1.603
1.876
1.708
0.858
1.487
-0.309
1.254
1.912
2.668
2.516
3.051
-0.198
0.203
0.191
1.658
0.663
3.354
3.676
3.499
0.177
0.843
D10-3-46_
3.597
1.523
0.984
1.996
1.298
0.013
-0.528
1.305
3.377
1.088
1.561
1.013
2.1
-0.362
0.067
-0.345
0.636
0.728
2.585
2.804
2.941
0.334
0.801
D2-9-39_
3.852
0.73
1.192
1.088
1.704
1.108
0.607
1.857
1.848
2.011
2.161
2.069
2.61
0.365
1.324
0.195
1.38
1.221
2.735
3.512
3.563
0.884
2.717
E4-9-39_
3.7
1.314
1.465
1.315
1.667
1.184
1.316
1.432
1.982
2.593
2.348
1.602
2.899
1.163
1.107
-0.113
1.248
0.904
2.608
3.122
3.248
1.221
2.272
Total number of rows: 339 Table truncated, full table size 48 Kbytes .Table 2: Targets that do not overlap with CpG islands header descriptions
ID_REF
nonCpG TFIIB
nonCpG TFIIEa
nonCpG RNAPIICTD
nonCpG NC2a
nonCpG TAF1
nonCpG TAF4
nonCpG TAF7
nonCpG TAF12
nonCpG TAF10
nonCpG CBP_p300
nonCpG TRRAP
nonCpG PCAF
nonCpG SNAP19
nonCpG SNAP43
nonCpG SNAP45
nonCpG SNAP50
nonCpG SNAP190
nonCpG Bdp1
nonCpG Brf1
nonCpG RNAPIII
nonCpG UBF
nonCpG RPA116
nonCpG PAF53
Data table
ID_REF
nonCpG TFIIB
nonCpG TFIIEa
nonCpG RNAPIICTD
nonCpG NC2a
nonCpG TAF1
nonCpG TAF4
nonCpG TAF7
nonCpG TAF12
nonCpG TAF10
nonCpG CBP_p300
nonCpG TRRAP
nonCpG PCAF
nonCpG SNAP19
nonCpG SNAP43
nonCpG SNAP45
nonCpG SNAP50
nonCpG SNAP190
nonCpG Bdp1
nonCpG Brf1
nonCpG RNAPIII
nonCpG UBF
nonCpG RPA116
nonCpG PAF53
F10-2-46_
0.949
0.288
0.111
0.234
-0.145
-0.15
0.284
0.278
0.717
0.732
-0.067
-0.124
0.266
0.018
1.757
-0.214
-0.461
-0.342
0.052
0.284
-0.226
0.147
0.187
E2-9-46_
0.963
-0.183
0.585
0.164
-0.386
0.039
0.272
0.076
0.305
1.067
-0.01
0.237
-0.019
0.734
0.226
0.016
0.245
0.51
0.103
0.732
0.545
0.121
-0.143
A1-2-39_
0.975
0.308
0.421
0.465
-0.084
0.035
0.062
0.029
0.611
1.158
0.045
0.372
0.374
0.862
0.855
0.245
0.267
0.293
0.282
0.783
0.365
0.153
0.146
B12-10-46_
0.982
0.565
0.359
0.354
0.466
-0.302
0.137
-0.27
1.011
1.035
0.166
-0.608
1.409
-0.407
-0.667
-0.117
-0.087
0.251
-0.086
0.171
0.081
-0.439
-0.517
E1-10-39_
0.993
0.435
0.188
0.053
-0.159
-0.041
0.606
0.587
0.643
1.805
0.08
-0.182
-0.011
0.845
0.794
-0.044
0.615
0.376
0.241
0.934
0.415
-0.194
-0.243
B8-2-39_
1.007
0.925
0.434
0.793
-0.086
0.656
1.11
0.726
1.307
1.447
0.028
1.305
1.082
1.395
2.274
-0.843
0.032
0.564
0.646
1.587
0.59
-0.161
0.481
F10-1-46_
1.051
0.364
0.364
0.401
-0.028
-0.13
0.386
0.421
1.127
1.53
0.149
0.584
0.36
0.869
0.783
-0.351
0.128
0.324
0.295
0.945
0.667
-0.057
0.055
G7-2-39_
1.056
0.936
0.475
0.438
0.193
-0.265
-0.814
-0.329
0.515
-0.163
0.444
0.269
0.01
0.546
0.191
-0.073
0.163
0.052
0.06
0.318
0.242
1.072
-0.053
B12-6-39_
1.07
0.881
0.334
1.262
0.641
0.511
-0.487
0.418
0.623
0.941
0.2
0.032
0.005
-0.363
-0.433
0.108
0.161
-0.011
-0.043
0.098
0.577
0.106
0.612
C3-2-39_
1.074
0.166
0.011
-0.051
-0.09
-0.359
-0.037
-0.015
0.831
0.906
-0.418
-0.114
0.187
0.022
0.537
-0.468
-0.394
-0.224
0.117
0.521
0.567
-0.364
-0.224
G3-9-39_
1.113
1.9
0.825
0.295
0.921
0.143
0.083
-0.498
0.95
0.434
1.253
1.562
1.949
1.114
1.33
-0.26
-0.224
0.03
0.499
0.949
0.354
0.936
-0.039
H1-9-39_
1.121
-0.445
0.107
-0.238
-0.04
-0.409
-0.182
-0.585
0.71
0.337
-0.228
-0.137
0.327
-0.208
-0.534
0.029
-0.452
-0.336
0.044
0.03
-0.235
-0.6
-0.747
G9-7-46_
1.123
0.701
0.783
0.646
-0.102
-0.24
0.163
-0.252
0.745
0.893
-0.273
0.537
-0.215
0.738
0.065
-0.777
0.508
-0.087
0.137
0.99
0.075
-0.218
-0.184
D2-10-39_
1.132
0.553
0.552
0.755
-0.017
1.084
2.275
2.149
1.403
3.596
0.404
1.034
1.625
2.039
1.871
0.213
1.537
1.612
0.199
1.613
1.295
0.442
0.668
C10-10-46_
1.153
0.413
0.447
1.287
0.327
0.382
-0.166
0.942
1.241
0.795
0.494
0.475
0.674
0.322
0.18
-0.02
1.62
0.289
0.324
0.455
0.757
0.895
1.396
G10-10-39_
1.167
0.084
0.347
0.122
0.012
0.502
0.887
0.657
1.085
1.674
-0.172
1.281
0.224
0.799
1.3
0.13
0.503
0.707
0.26
1.328
0.976
-0.318
-0.553
E10-2-46_
1.174
0.331
0.22
0.601
0.363
0.287
0.123
0.555
1.46
1.637
0.215
0.277
0.679
0.246
0.262
-0.08
0.239
0.186
0.17
0.523
0.887
0.556
0.809
D7-10-46_
1.196
0.321
0.341
0.948
0.288
0.554
0.563
0.45
1.001
1.253
0.441
1.369
0.62
-0.017
0.074
-0.153
0.447
0.332
-0.109
0.248
0.837
1.122
2.025
F5-8-46_
1.199
0.187
0.245
-0.55
-0.148
-0.25
-0.12
-0.529
0.702
0.908
0.263
-0.189
-0.084
0.256
0.433
-0.121
-0.487
-0.225
0.468
0.424
0.423
-0.319
-0.009
F3-3-39_
1.312
0.17
0.141
0.561
0.563
-0.049
-0.261
0.191
1.553
1.363
0.254
0.706
0.727
-0.363
0.392
-0.143
0.092
-0.174
0.092
0.575
0.809
0.253
0.377
Total number of rows: 394 Table truncated, full table size 56 Kbytes .
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