Table of Contents
PPT Slide
Outline
Biology
Chemical Reaction
Enzymatic catalysis
Enzymatic catalysis
Inhibition/Activation
Gene expression
Metabolic Step
Metabolic Pathway: Proline Biosynthesis
Transcriptional Regulation
Methionine Biosynthesis in E.coli
Methionine Biosynthesis in S.cerevisiae
Alternative methionine pathways
Shortcut Representation
High-level Abstraction
Levels of resolution
Phosphate utilization in yeast
Multiple levels of regulation
Transport
PPT Slide
Graph Theory (simple!)
Terminology
Paths and Circuits of a Graph
Example
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Reactions and compounds as graphs
Requirements: Network navigation
Requirements: Network analysis
Databases & systems available
KEGG
KEGG
KEGG - search & compute
KEGG Query & result
E.Coli operon table
Select trp operon
Launch pathway search
Search window
Result of pathway search
path: eco00040
EcoCyc
EcoCyc
E.Coli metabolic overview
Query = 2.7.2.4
Query = 2.7.2.4 Enzymatic reaction of: aspartokinase III L-aspartate + ATP <=> L-aspartyl-4-P + ADP
BRENDA
PathDB
PFBP (Protein Function and Biochemical Pathways )
PFMP: Pathway Editor Functionality
PFBP suite
Queries : Pathway Analysis
PPT Slide
PFBP Pathway Builder : semi-automated annotation
Pathway Builder Result
Databases containing information on other types of biochemical processes
Metabolic databases - URLs
What is required
What’s next?
Analysis of gene expression data
Subgraph extraction
Maximal Pathway extracted from a cluster of cell-cycle regulated genes
Analysis of Gene Expression Data
The PFBP people
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Author: David Gilbert and Jacques van Helden
Email: drg@cs.city.ac.uk
Home Page: http://www.cs.city.ac.uk/~drg
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