Pathos: a web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry

Leader, D.P. , Burgess, K., Creek, D. and Barrett, M.P. (2011) Pathos: a web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry. Rapid Communications in Mass Spectrometry, 25(22), pp. 3422-3426. (doi:10.1002/rcm.5245)

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Abstract

This work describes a freely available web-based facility which can be used to analyse raw or processed mass spectrometric data from metabolomics experiments and display the metabolites identified – and changes in their experimental abundance – in the context of the metabolic pathways in which they occur. The facility, Pathos (http://motif.gla.ac.uk/Pathos/), employs Java servlets and is underpinned by a relational database populated from the Kyoto Encyclopaedia of Genes and Genomes (KEGG). Input files can contain either raw m/z values from experiments conducted in different modes, or KEGG or MetaCyc IDs assigned by the user on the basis of the m/z values and other criteria. The textual output lists the KEGG pathways on an XHTML page according to the number of metabolites or potential metabolites that they contain. Filtering by organism is also available. For metabolic pathways of interest, the user is able to retrieve a pathway map with identified metabolites highlighted. A particular feature of Pathos is its ability to process relative quantification data for metabolites identified under different experimental conditions, and to present this in an easily comprehensible manner. Results are colour-coded according to the degree of experimental change, and bar charts of the results can be generated interactively from either the text listings or the pathway maps. The visual presentation of the output from Pathos is designed to allow the rapid identification of metabolic areas of potential interest, after which particular results may be examined in detail.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Burgess, Dr Karl and Leader, Dr David and Barrett, Professor Michael and Creek, Dr Darren
Authors: Leader, D.P., Burgess, K., Creek, D., and Barrett, M.P.
College/School:College of Medical Veterinary and Life Sciences > School of Life Sciences
College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Rapid Communications in Mass Spectrometry
ISSN:0951-4198
ISSN (Online):1097-0231
Published Online:17 October 2011
Copyright Holders:Copyright © 2011 John Wiley and Sons
First Published:First published in Rapid Communications in Mass Spectrometry 25(22):3422-3426
Publisher Policy:Reproduced in accordance with the copyright policy of the publisher

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