Biological interpretation

Moderators: Suzan WOPEREIS, Ben VAN OMMEN (TNO, Zeist)

Background:

After having ‘walked’ through the metabolomics pipeline without failure and having found those effects caused by the nutritional intervention and identified all the relevant metabolites, it is essential to ‘understand’ what the data is telling you in order to make your study to a success. At the moment tools for the biological interpretation of metabolomics data are scarce. In this session we shall discuss how to improve the biological interpretation of metabolomics data.

Goal:

We will decide whether it would be useful for NuGO to create an intergrated workbench for metabolomics data interpretation, according to the Genepattern model (http://www.broad.mit.edu/cancer/software/genepattern/).

Approach:

Discussion of the following issues:

1.      Inventory of available tools

• Pathway analysis (Pathvisio, Metacore, other open source developed tools)
• From pathways to processes (Metabo-go ontology)
• Network biology (Metacore, …)
• Multi-layer omics tools, data fusion

2.      Nutritional phenotype issues

• Plasma biochemistry – how can we relate the phenotype (commonly expressed as specific plasma biochemical measurements) to our metabolomics results?
• Study design: challenges, plasma vs. urine, do we need a standard run in diet?
• Biology driven analysis – Are we really measuring those compounds that can provide us the answers to our research questions or should we create a list with all relevant metabolites that (at least) should be measured?
• Exploit “confounders” – Do we need an endocrine platform? Do we need to create subgroups based on geno- /phenotype? What factors influence the nutritional metabolome?
• Fluxes – do we need information on the dynamics of metabolites for the biological interpretation?
• How to separate endo- and exo–(food) metabolome
• Validation studies – how can we validate our biological interpretation?

3.      Towards and integrated workbench?

·        Is it useful to create an integrated workbench for metabolomics data interpretation, according to the Genepattern model?

Result:

An overview of the approaches and tools for biological interpretation of metabolomics studies used by the participants. Decision on how biological interpretation in nutritional metabolomics studies can be improved and whether it would be useful if NuGO has an integrated workbench for metabolomics data interpretation.

Recent publications:
We strongly encourage all the participants of this session to have a look at the selection of recent publications prepared by the Moderators and Organizing Committee. Each participant of this session should have critical ideas on the present state of the art, and will actively contribute to the elaboratation of recommendations when taking part to this session.

The pdf files for the session biological interpretation can be found at:
pdf files_biological interpretation

The slides shown during this session can be found in the attachments.

	Biological interpretation Introduction Wopereis.pdf	870 KB
	Biological interpretation session Wopereis.pdf	1205 KB
	Let's have a dream_van Ommen.pdf	90 KB