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.
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
|