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Pathway Mining

Identify most changed pathways, reactions and compartments in a dataset
Martin A. Fitzpatrick

Introduction

In untargeted metabolic studies it is often useful to determine the key areas of metabolic regulation within a system. Pathomx supports pathway-based mining of experimental data, using a number of different scoring algorithms, which has the added benefit of proving context for the identified change.

Quick start

To enable pathway pruning, simply load data as above then enable pruning via the menubar.

Starting with the entire network of metabolic pathways in the database, each pathway will be scored according to the chosen method and lower-scoring pathways removed from the view up to the set pruning threshold. The remaining pathways are displayed, giving an overview of the key pathways in the system. Note that pruning obeys the 'Show Selected Pathways...' settings which can be useful to link disparate pathways into a regulated whole.

The scoring algorithm can be altered from the 'Pruning settings...' dialog. Scoring can be based on upregulation, downregulation, overall change and by the number of identified metabolites in the sample. Adjusting scores relative to the number of metabolites in a pathway removes the bias towards larger pathways (although this is often preferable for interpretation). You can adjust the pruning threshold from the data toolbar.

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