Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale

Shmelkov, Evgeny; Tang, Zuojian; Aifantis, Iannis; Statnikov, Alexander

doi:10.1186/1745-6150-6-15

Biology Direct

Table 2 Gold standards for each transcription factor (TF).

From: Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale

TF	Gold Standard ID#	Genes bound by the TF are obtained from	Genes that are downstream of the TF are obtained from
			Study	Analyzed to find genes that are
AR	I			• differentially expressed between DHT treated (for 4 hr.) and control samples
	II	Wang et al. [22]	Wang et al. [18]	• differentially expressed between DHT treated (for 16 hr.) and control samples
	III			• differentially expressed between DHT treated (for 4 hr. and 16 hr.) and control samples
BCL6	I	Basso et al. [9]		• differentially expressed between siRNA treated and control samples
	II	Ci et al [20]	Basso et al. [9]	• differentially expressed between siRNA treated and control samples
	III	Basso et al. [9]		• up-regulated in siRNA treated samples
	IV	Ci et al [20]		• up-regulated in siRNA treated samples
MYC	I		Cappellen et al. [11]	• differentially expressed between siRNA treated and control samples
	II	Margolin et al. [14]		• down-regulated in siRNA treated samples
	III		Bild et al. [10]	• differentially expressed between MYCexpressing and control samples
	IV			• up-regulated in MYC-expressing samples
NOTCH1	I		Margolin et al. [14]	• differentially expressed between GSI treated and control samples
	II			• down-regulated in GSI treated samples
	III	Margolin et al. [14]	Palomero et al. [15]	• differentially expressed between GSI treated and control samples
	IV			• down-regulated in GSI treated samples
	V		Sanda et al. [17]	• differentially expressed between GSI treated and control samples
	VI			• down-regulated in GSI treated samples
RELA	I		Espinosa et al. [19]	• differentially expressed between NBD treated and control samples
	II	Kasowski et al. [13]		• down-regulated in NBD treated samples
	III		Kasowski et al. [13]	• differentially expressed between TNF-α treated and control samples
	IV			• up-regulated in TNF-α treated samples
STAT1	I	Robertson et al. [21]	Pitroda et al. [16]	• differentially expressed between shRNA treated and control samples
	II			• down-regulated in shRNA treated samples
TP53	I	Wei et al. [23]	Chau et al. [12]	• differentially expressed between shRNA and control samples
	II			• down-regulated in shRNA treated samples

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ISSN: 1745-6150

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