Transcript Biochemical Pathways

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Fig 1. Metabolic Pathways
ExPASy, http://www.expasy.org
/cgi-bin/show_thumbnails.pl, founded
by Roche Applied Science.
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Metabolic Pathways
It is the pathway to show how to generate energy and remove
metabolite for a body.
Signal Transduction Pathways
It is the pathway to show how to control the behaviors of a cell
in terms of time and location with the signals like hormones.
Regulatory Pathways (Gene Regulatory Network)
It is the pathway to show how to adapt to the change of environment
based on the principles encoded in hereditary materials (e.g. DNA).
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Signal Transduction
1 Glucoses + 2 ATP
Metabolism
Regulation
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4 ATP + 2 Pyruvate + 2 NADH
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To understand the mechanism of organism
• It provides the guidance for biologists to design experiments.
• It helps pharmacist to design drugs easier.
• It makes us know the difference of mechanism between species.
Enable us to do the simulation
• It saves time and money for biologists to do experiments.
• It predicts the behaviors by a special treatment for an organism.
• It waives the dangers to try a new drug on patients.
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Data
Accumulation
Data
Repository
Data
Exchange
Data
Inference
Literature
Mining
Pathway
Databases
Database
Integration
Pathway
Query
Pathway
Diagrams
Pathway
Representation
Standard
Format for
Pathways
Pathway
Reasoning
Graphical
Modelers
Simulation
Cell
Behaviors
Simulation
Management
Tools
Hot Issues
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ACTIVATOR activate ACTIVATEE
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Moustafa M. Ghanem et al.
(UK)
Regular Expression
Pattern Matching
SVM Classifier
Yizhar Regev et al.
(Israel & USA)
Rule-based Pattern Matching
Text
Mining
Min Shi et al.
(Singapore)
Manually chosen keywords
Keywords Distance
B. Chen
(Personal Communication)
Alexander S. Yeh et al. (2003)
“Evaluation of text data mining for database curation: lessons
learned from the KDD Challenge Cup”
Bioinformatics, Vol. 19 Suppl. 1 2003, pages i331–i339
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Regular Expression
SVM Classifier
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Complete
Medium
Minimal
Medium
Minimal
Medium
plus
aminoacids
Minimal
Medium
plus vitamis
Minimal
Medium
plus
nucleotides
1
2
3
4
5
6
7
1
+
+
+
+
2 3 4 5 6 7
+
+
+
+
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+
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+ + + + + + -
1
2
3
4
5
6
7
1
+
+
+
+
2 3 4 5 6 7
+
+
+
+
+
+
+
+ + + + + + -
1
2
3
4
5
6
+wt
GLU
-
-
-
-
-
-
+
NAG
-
-
-
-
-
+
+
ORN
-
-
-
+
+
+
+
CIT
-
+
+
+
+
+
+
ARG
+
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+
1
2
3
4
5
6
W
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+
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+
-
X
-
-
-
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-
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Y
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+
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-
-
Z
-
-
-
+
-
-
His
+
+
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+
+
1
2
3
4
5
6
W
-
+
+
+
+
-
X
-
-
-
-
-
-
Y
-
+
-
+
-
-
Z
-
-
-
+
-
-
His +
+
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+
+
+
1
2
3
4
5
6
W
-
+
+
+
+
-
X
-
-
-
-
-
-
Y
-
+
-
+
-
-
Z
-
-
-
+
-
-
His +
+
+
+
+
+
Remember the basic rule:
1
2
3
4
5
6
W
-
+
+
+
+
-
X
-
-
-
-
-
-
Y
-
+
-
+
-
-
Z
-
-
-
+
-
-
His +
+
+
+
+
+
1
2
3
4
5
6
W
-
+
+
+
+
-
X
-
-
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-
-
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Y
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+
-
+
-
-
Z
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-
-
+
-
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His +
+
+
+
+
+
Mutants 1 and 6 do this: they block the
final step.
1
2
3
4
5
6
W
-
+
+
+
+
-
X
-
-
-
-
-
-
Y
-
+
-
+
-
-
Z
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-
-
+
-
-
His +
+
+
+
+
+
Thus, the pathway so far is W -> His, with
1 and 6 affecting this step.
1
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3
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6
W
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+
+
+
+
-
X
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Y
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+
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Z
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-
-
+
-
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His +
+
+
+
+
+
X
4
2
Z
Y
3, 5
1, 6
W
1
2
3
4
5
6
X
-
-
-
-
-
-
Z
-
-
-
+
-
-
Y
-
+
-
+
-
-
W
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+
+
+
+
-
His +
+
+
+
+
+
¿?
His
X
4
2
Z
Y
3, 5
W
1
6
3
5
2
4
X
-
-
-
-
-
-
Z
-
-
-
-
-
+
Y
-
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-
+
+
W
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+
+
+
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His +
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+
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+
+
1, 6
¿?
His