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Table 2 Comparison of predictions of regulatory interactions made by the algorithm presented here, results obtained from the paper of Lee et al. [6] and the data from YEASTRACT database for selected genes (cell cycle – ACE2, SKN7, SWI4, SWI5, DNA/RNA/protein synthesis -, ABF1, RAP1).

From: Supervised inference of gene-regulatory networks

  Lee et al. This paper YEASTRACT
ACE2 FKH2 FKH2 FKH2
  GAT1 GAT1 GAT1
  NDD1 NDD1 -
  MCM1 MCM1 MCM1
  SFL1 SFL1 SFL1
  YAP1 - -
SKN7 ROX1 ROX1 ROX1
  NRG1 NRG1 NRG1
  YAP1 YAP1 YAP1
  SFL1 - SFL1
  SOK2 SOK2 SOK2
  - FKH1 FKH1
SWI4 MBP1 - MBP1
  MCM1 MCM1 MCM1
  MOT3 MOT3 MOT3
  NDD1 - -
  SOK2 SOK2 SOK2
  SWI4 SWI4 -
  SWI6 SWI6 -
  - CRZ1 -
  - DAL82 -
  - DOT6 -
  - FZF1 -
  - GLN3 GLN3
  - MAL33 -
  - MSN2 MSN2
  - RCS1 -
  - RFX1 RFX1
  - RGT1 RGT1
  - RTG3 RTG3
  - SKO1 SKO1
  - STP2 -
  - THI2 -
  - MDD1 -
SWI5 ASH1 ASH1 ASH1
  FKH2 FKH2 FKH2
  GAT1 - GAT1
  GAT3 GAT3 GAT3
  MCM1 MCM1 MCM1
  NDD1 NDD1 -
  SFL1 - SFL1
ABF1 IME4 IME4 IME4
  FHL1 FHL1 FHL1
  MSN1 MSN1 MSN1
  DAL81 DAL81 DAL81
  PHO2 PHO2 PHO2
  PUT3 PUT3 PUT3
  STP1 STP1 STP1
  RIM101 RIM101 RIM101
  - FZF1 -
  - HAP2 HAP2
RAP1 GAT1 GAT1 GAT1
  RPH1 RPH1 RPH1
  RCS1 RCS1 RCS1
  MSN4 MSN4 MSN4
  SIP4 SIP4 SIP4
  RAP1 RAP1 -
  HSF1 HSF1 -
  - SUM1 -
  - RSF2 -
  - HAP4 -
  - GAT3 -
Total 40 56 -
Confirmed by YEASTRACT 32 37  
Not confirmed by YEASTRACT 8 19  
Present in Lee et al. - 34