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Table 1 Scores of computational search for activity-dependent transcription factor binding sites

From: A comparative genomics approach to identifying the plasticity transcriptome

  Mouse Human Homologuea
Measure Promoterb Intergenicc Scored Promoterb Intergenicc Scored Completee Conservedf Scoreg
Total genes 18071 13475   19794 15178   13365 516  
CREB targets 1050 279 0.64 1389 388 0.64 830 356 0.83
zif268 targets 1382 200 0.81 1203 244 0.74 1136 166 0.56
% CREB genes 5.81% 2.07%   7.02% 2.56%   6.21% 2.66%  
% zif268 genes 7.65% 1.48%   6.08% 1.61%   8.50% 1.24%  
  1. a The homologue dataset was contructed using the Homologene resource on the NCBI website (http://www.ncbi.nih.gov).
  2. b The promoter region is the area from -1,000 to 200 bp relative to transcription start.
  3. c Intergenic regions refer to an area 50,000 bp away from transcription start. Fewer intergenic regions are available than genes because of gaps in sequencing.
  4. d The score is determined by the positive predictive value which is a conservative estimate of the fraction of found transcription factor binding sites that are true hits. It is calculated as (%Observed - %Intergenic)/(%Observed).
  5. eThe complete homologue numbers refer the the number of human/mouse homologous pairs identified using the Homologene resources.
  6. f The conserved dataset is a subset of the Homologene dataset that consists of only those genes for which homologous pairs contain a conserved binding site.
  7. g The quality is determined by the positive predictive value which is a conservative estimate of the percentage of found transcription factor binding sites that are true hits. It is calculated as (%Conserved Observed - %Predicted Conserved)/(%Conserved Observed).