Algorithms and Parameters

1.Algorithm and implementation

We are working on incoporating SAMBA into the EXPANDER system. For a very early version of the SAMBA search algorithm see our computational paper from ISMB 2002.

2. Parameters

The translation function we have applied to physical measurements of different sources are specified in the table below. The tranlation function are constant outside the scope of the specified exterme values, and linear between them. Note that this "soft discretization" process is applied to the normalized data.

1.Algorithm and implementation

We are working on incoporating SAMBA into the EXPANDER system. For a very early version of the SAMBA search algorithm see our computational paper from ISMB 2002.

2. Parameters

The translation function we have applied to physical measurements of different sources are specified in the table below. The tranlation function are constant outside the scope of the specified exterme values, and linear between them. Note that this "soft discretization" process is applied to the normalized data.

Num |
Name |
Data Source |
Upper limit |
Lower limit |

1 |
Induction 1 |
Expression |
p =1 for x>2.8 |
p=0 for x<2 |

2 |
Induction 2 |
Expression |
p =1 for x>2.3 |
p=0 for x<1.3 |

2 |
Induction 3 |
Expression |
p =1 for x>1.5 |
p=0 for x<0.9 |

4 |
Induction 4 |
Expression |
p =1 for x>1.2 |
p=0 for x<0.6 |

5 |
Repression 1 |
Expression |
p=1 for x<-2.8 |
p=0 for x>-2 |

6 |
Repression 2 |
Expression |
p=1 for x<-2.3 |
p=0 for x>-1.3 |

7 |
Repression 3 |
Expression |
p=1 for x<-1.5 |
p=0 for x>-0.9 |

8 |
Repression 4 |
Expression |
p=1 for x<-1.2 |
p=0 for x>-0.6 |

9 |
Binding 1 |
TF profile |
p=1 for x<0.0005 |
p=0 for x>0.001 |

10 |
Binding 2 |
TF profile |
p=1 for x<0.001 |
p=0 for x>0.005 |

11 |
Binding 3 |
TF profile |
p=1 for x<0.005 |
p=0 for x>0.01 |

12 |
Binding 4 |
TF profile |
p=1 for x<0.01 |
p=0 for x>0.05 |

13 |
Sensitivity 1 |
Phenotype |
p=1 for x>20 |
p=0 for x<10 |

14 |
Sensitivity 2 |
Phenotype |
p=1 for x>50 |
p=0 for x<40 |