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Table 1 Data used to evaluate ChIPXpress

From: ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking

TF Cell type Species Experiment type Source # of GS target genes
Oct4 ESC Mouse ChIP-seq GSE11724  
Oct4 ESC Mouse TFP - knockdown GSE4189  
Oct4 ESC Mouse    3010, 1303, 1224
Jarid2 ESC Mouse ChIP-chip (T) GSE19167  
Jarid2 ESC Mouse TFP - knockout GSE19165  
Jarid2 ESC Mouse    1199, 370, 872
Gli3 Limbbud Mouse ChIP-chip (P) GSE11062  
Gli3 Limbbud Mouse TFP - knockdown GSE11062  
Gli3 Limbbud Mouse    826, 712, 676
Esrrb ESC Mouse ChIP-seq GSE11431  
Esrrb ESC Mouse TFP - knockdown GSE13212  
Esrrb ESC Mouse    4826, 1591, 1377
Nanog ESC Mouse ChIP-seq GSE11431  
Nanog ESC Mouse TFP - knockdown GSE4189  
Nanog ESC Mouse    701, 560, 712
HIF1A U87 Human ChIP-chip (P) GSE18499  
HIF1A U251 Human TFP - knockdown GSE7835  
HIF1A U251 Human    794, 1192, 725
ESR1 MCF7 Human ChIP-chip (T) GSE10800  
ESR1 MCF7 Human TFP - overexpress GSE11324  
ESR1 MCF7 Human    153, 564, 91
MYC Helas3 Human TFP - knockdown GSE5823  
MYC Helas3 Human ChIP-seq ENCODE-UTA  
MYC Helas3 Human    768, 879, 1055
MYC MCF7 Human TFP - knockdown GSE11791  
MYC MCF7 Human ChIP-seq ENCODE-UTA  
MYC MCF7 Human    836, 305, 901
TFAP2C MCF7 Human TFP - knockout GSE8640  
TFAP2C MCF7 Human ChIP-seq GSE21234  
TFAP2C MCF7 Human    3289, 2302, 3504
  1. TFP TF perturbation gene expression data, P Affymetrix Promoter array, T Affymetrix Tiling array, GS gold standard constructed by intersecting TF bound genes in ChIPx data with differentially expressed genes in TF perturbation experiments. For each TF, three sets of GS were constructed using three different peak callers. The table shows the number of GS target genes corresponding to TileProbe, MAT, TileMap for ChIP-chip data (left to right) and CisGenome, MACS, and Original for ChIP-seq data (left to right).