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

BMC Bioinformatics

Table 1 Data used to evaluate ChIPXpress

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

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).

ISSN: 1471-2105