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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