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Series GSE6738 Query DataSets for GSE6738
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)
GSM151755 TFIIB
GSM151756 TFIIEa
GSM151757 RNAPIICTD
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.




Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE6738_RAW.tar 34.0 Mb (http)(custom) TAR (of GPR)

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