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The Diversity and Integration of Biological Network Motifs. Seminars in Bioinformatics Martin Akerman 31/03/08. Biological Networks. Questions: Which are the most common motifs among biological networks? How do these motifs interrelate?. Biological Network motifs.
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The Diversity and Integration of Biological Network Motifs
Seminars in Bioinformatics
Martin Akerman
31/03/08
Single Input Model (SIM)
Autoregulation (AR)
Dense Overlapping Regulon (DOR)
Feed Forward Loops (FFL)
Regulating and Regulated Feedback Loops (RFL)
BiFan
Diamond
Cascade
LastIn FirstOut (LIFO) Program
Kxz1
Kxz2
[X]
Kxz3
Kxz3
Kxz2
[Y]
Kxz1
[Z1]
[Z2]
[Z3]
Kxz1>Kxz2>Kxz3K’xz1<K’xz2<K’xz3
Time
Noxious Chemicals
Nose Touch
Nose Touch
FLP
ASH
AVD
AVA
Backward movement
The change in voltage of Y
X1
X2
The change in voltage of Z
Y
Z
Bacillus Subtilis sporuation process
FFLs and SIMs are integrated within DORs
Where are the XYZ ?
A Master Regulators Layer (lots of AutoReg.)
A single DOR Layer
The E.coli Transcription Network (partial)
Popular Motifs in Signal Transduction Cascades
X
X1
X2
Y1
Y2
Y1
Y2
Z
BiFan
Diamond
Generalization of DOR
X1
X2
X
X1
X2
Multilayer Perceptrons
(multiDORs)
Y1
Y2
Y1
Y2
Y1
Y2
Z
Z1
Z2
Z1
Z2
X2
X2
P
X1
X1
P
Y2
Y2
P
Y1
Y1
P
Z2
Z2
P
Z1
Z1
P
X1
X2
Y
At Steady State
X2
0.5
,
Activation Threshold
X1
0.5
“AND” gate
“OR” gate
X1
X2
X1
X2
Y
Y
X2
X2
0.5
0.5
X1
0.5
X1
0.5
“OR” gate
X1
X2
1.5
1.5
0.7
0.7
Y1
Y2
Z
Y1
Y2
2
2
Z
“AND” gate
X1
X2
1.5
1.5
0.7
0.7
Y1
Y2
Z
Y1
Y2
0.6
0.6
Z
X1
X2
1.5
1.5
0.7
0.7
Y1
Y2
Z
Y1
Y2
2
3
Z
X1
X2
1.7
0.7
1.7
0.7
Z
Y1
Z
Y2
Y1
Y2
2
3
Z
Z
X
Y
X
Y
Power
Heater
Temperature

(Fast) ProteinProtein Interactions
Thermostat
(Slow) Transcriptional Interactions
Cdc20 oscillator controls Cell Cycle
Mutation of the Drosophila CWO gene
The TF expression profile in a
developing Drosophila embryo
Twonode Feedback Loops
X
Y
X
Y
Regulating Feedback Loops
X
Y
X
Y
Z
Z
Double Negative Loops
Double Positive Loops
Z
Z
X
Y
X
Y
Regulated Feedback Loops
Regulated Feedback Loops as a Memory Element
Cascades
X
Y
Z
X
Y
Z