U N I V E R S I T Ä T S M E D I Z I N B E R L I N

Analysis of pahtways in metabolic networksBenjamin Menküc, Charité Universitätsmedizin, Computational Systems Biochemistry

Organisation

• Introduction

• Description of a metabolic network

• Validation methods

• Metabolic Network Navigator, a software for analysing metabolic networks

– Importing data

– Browsing data

– Network creation and graphical representation

– Path finding

• Outlook

Introduction

• Organisms are modelled as metabolic networks in order to predict complex behaviour (i.e. in absence of some metabolites)

• Possible errors during modelling– Non-existent biochemical knowledge– Human errors

• Validation, because simulation requires complete/consistent network– Gaps in biochemical knowledge are filled by reasonable assumptions– Identify and eliminate human errors by using well established biochemical

knowledge

• Analysis - working with the network– Pathways from one metabolite to another– Producibility of metabolites under certain conditions– Successor metabolites

Metabolic Navigator

Description of a metabolic network

Organism

Reaction

Compartment

Compound

Metabolite

User Datasets Kegg Data

Metabolic Network Navigator – Importing data

• Importing user datasets and Kegg data– Copy user datasets to C:\datasets\...– Copy Kegg data files to the following directories

compound -> C:\kegg\ligand\compound\reaction -> C:\kegg\ligand\reaction\

– Press „Do all“ to import all data and calculate linked reactions (neccessary for some algorithms later)

Metabolic Network Navigator – Browsing data

• It is possible to browse and search the imported data (compounds, reactions, datasets)

Metabolic Network Navigator – Creating networks

• A metabolic network consists of metabolites (nodes) and reactions (edges)

• Useful for– Finding paths from one metabolite to another– Checking the scope of a metabolite in a specific organism– Finding errors– Etc…

• Uses kegg-rpairs to reasonably reduce networks complexity. Different apply rules:

Metabolic Network Navigator – Creating networks

• Chose reactions and start metabolite

• Blacklist some metabolites for network simplicity

Metabolic Network Navigator – Creating networks

• Finally create the network

Metabolic Network Navigator – Creating network graphs• Just press the „graph“ button

Metabolic Network Navigator – Finding paths 1/2

• Chose a start- and end-metabolite• Chose the number of generations for the network

1

2 3

Metabolic Network Navigator – Finding paths 2/2

• Browse all possible paths

Outlook

• Graph– Highlight paths in network– Graph view of paths– Grouping compartments together– Display reaction names

• Network algorithms– Trace atoms (using Kegg rdm data)

• General– Vista compatibility– Improved „Metabolic Walker“

Thank You for listening!

And thanks to Sabrina and Christoph for their kind support