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Table 2 Peak features obtained using the individual, union and intersection methods

From: An improved ChIP-seq peak detection system for simultaneously identifying post-translational modified transcription factors by combinatorial fusion, using SUMOylation as an example

  Peak # TFBS peak # TFBS #
Methods Total Promoter Total Promoter Total Promote
MACS = M 53,972 10,282 15,428 3,934 110,779 27,615
CisGenome = C 32,158 12,069 7,153 4,640 30,828 5,322
T-PIC = T* 459,962 37,923 99,986 20,735 477,353 20,008
BayesPeak = B 241,257 35,349 102,905 9,188 220,182 48,710
M+C+T 465,103 31,096 100,484 15,352 460,753 39,449
M+T 460,503 38,023 100,417 20,775 477,996 22,042
M+C 65,605 32,588 17,643 7,400 120,964 54,569
C+T 462,622 43,355 100,284 20,735 478,565 22,008
M*C*T 20,349 9,834 4,834 3,604 20,525 3,860
M*T 50,655 17,246 15,274 9,312 128,473 10,526
M*C 20,525 9,852 4,863 3,612 20,643 3,874
C*T 30,158 11,914 6,780 4,637 29,616 4,956
  1. * p-value < 0.001