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Bioinformatics. 2015 Dec 1;31(23):3721-4. doi: 10.1093/bioinformatics/btv475. Epub 2015 Aug 13.

Determining conserved metabolic biomarkers from a million database queries.

Author information

1
Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA.
2
Department of Physics, University of California San Diego, La Jolla, CA 92093, USA.
3
Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA, Departments of Genetics and Medicine, Washington University School of Medicine, St. Louis, MO 63130, USA.
4
Pfizer Worldwide Research and Development, San Diego, CA 92121, USA and.
5
Scripps Center for Metabolomics, The Scripps Research Institute, La Jolla, CA 92037, USA, Departments of Chemistry, Molecular and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

Abstract

MOTIVATION:

Metabolite databases provide a unique window into metabolome research allowing the most commonly searched biomarkers to be catalogued. Omic scale metabolite profiling, or metabolomics, is finding increased utility in biomarker discovery largely driven by improvements in analytical technologies and the concurrent developments in bioinformatics. However, the successful translation of biomarkers into clinical or biologically relevant indicators is limited.

RESULTS:

With the aim of improving the discovery of translatable metabolite biomarkers, we present search analytics for over one million METLIN metabolite database queries. The most common metabolites found in METLIN were cross-correlated against XCMS Online, the widely used cloud-based data processing and pathway analysis platform. Analysis of the METLIN and XCMS common metabolite data has two primary implications: these metabolites, might indicate a conserved metabolic response to stressors and, this data may be used to gauge the relative uniqueness of potential biomarkers.

AVAILABILITY AND IMPLEMENTATION:

METLIN can be accessed by logging on to: https://metlin.scripps.edu

CONTACT:

siuzdak@scripps.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26275895
PMCID:
PMC4836397
DOI:
10.1093/bioinformatics/btv475
[Indexed for MEDLINE]
Free PMC Article

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