MBRole: enrichment analysis of metabolomic data

Chagoyen, Mónica; Pazos, Florencio

doi:10.1093/bioinformatics/btr001

Cited by 134 publications

(105 citation statements)

References 10 publications

(11 reference statements)

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“…The total list of metabolites was also analysed using the bioinformatic tool Metabolites Biological Role (MBRole; http:// csbg.cnb.csic.es/mbrole/) in order to identify over-represented or enriched biological pathways that could be putatively active (p-values < 0.05 were considered significant) (Chagoyen & Pazos, 2011). These pathway results were based on the Small Molecule Pathway Database (SMPDB; http://smpdb.ca) (Frolkis et al, 2010;Jewison et al, 2014).…”

Section: Metabolites Annotation and Bioinformatic Analysesmentioning

confidence: 99%

Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance (¹H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)

et al. 2015

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SUMMARYThe objective of this study was to contribute to the first comprehensive metabolomic characterization of the human sperm cell through the application of two untargeted platforms based on proton nuclear magnetic resonance ( 1 H-NMR) spectroscopy and gas chromatography coupled to mass spectrometry (GC-MS). Using these two complementary strategies, we were able to identify a total of 69 metabolites, of which 42 were identified using NMR, 27 using GC-MS and 4 by both techniques. The identity of some of these metabolites was further confirmed by two-dimensional C heteronuclear single-quantum correlation (HSQC) spectroscopy. Most of the metabolites identified are reported here for the first time in mature human spermatozoa. The relationship between the metabolites identified and the previously reported sperm proteome was also explored. Interestingly, overrepresented pathways included not only the metabolism of carbohydrates, but also of lipids and lipoproteins. Of note, a large number of the metabolites identified belonged to the amino acids, peptides and analogues super class. The identification of this initial set of metabolites represents an important first step to further study their function in male gamete physiology and to explore potential reasons for dysfunction in future studies. We also demonstrate that the application of NMR and MS provides complementary results, thus constituting a promising strategy towards the completion of the human sperm cell metabolome.

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Section: Metabolites Annotation and Bioinformatic Analysesmentioning

confidence: 99%

Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance (¹H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)

et al. 2015

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“…Metabolites with a VIP value > 1.0 and with an absolute p(corr) of > 0.4 were identified as potential biomarkers. To identify pathways affected by exposure to BDE-209 in the serum, we employed an overrepresentation test using MBRole (Chagoyen and Pazos, 2011). The p-values of the over-representation test were adjusted by controlling the false discovery rate (FDR).…”

Section: Statistical and Pathway Analysesmentioning

confidence: 99%

“…Higher levels of some amino acidrelated compounds (arginine, glycine, methionine, threonine, tyrosine, and N-acetylornithine), long-chain phospholipids (lysoPC a C14:0, PC ae C34:0, PC ae C36:0, and PC aa C42:2), and short-chain acylcarnitines (C3-OH and C4:1) were identifi ed in the exposed group (Kanehisa et al, 2008;Wishart et al, 2013). The related metabolic pathways of each metabolite were analyzed by MBRole (Chagoyen and Pazos, 2011). The over-representation test results show that carbohydrate and amino acid metabolism were upregulated, while lipid metabolism was downregulated (q-value < 0.05) (Tables 2 and 3).…”

Section: Fia-ms/ms-and Hilic-ms/ms-based Metabolomicsmentioning

confidence: 99%

The effects of early postnatal exposure to a low dose of decabromodiphenyl ether (BDE-209) on serum metabolites in male mice

2016

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-The toxicity of decabromodiphenyl ether (BDE-209) has been reported in several studies. However, there is not much known about the toxicological biomarkers that characterize BDE-209 exposure. In this study, we subcutaneously exposed mice to 0.025 mg/kg/day BDE-209 on postnatal days 1-5 and sacrificed the animals at 12 weeks of age (day 84). Flow injection analysis and hydrophilic interaction chromatography-triple quadrupole mass spectrometry were used to determine the serum metabolomes of these mice in order to characterize the effects of BDE-209 exposure. Data analysis showed a good separation between control and exposed mice (R 2 = 0.953, Q 2 = 0.728, and ANOVA of the crossvalidated residuals (CV-ANOVA): P-value = 0.0317) and 54 metabolites were identified as altered in the exposed animals. These were selected using variable importance (VIP) and loadings scaled by a correlation coefficient criteria and orthogonal partial least squares discriminant analysis (OPLS-DA). BDE-209-exposed mice showed lower levels of long-chain acylcarnitines and citrate cycle-related metabolites, and higher levels of some amino acids, long-chain phospholipids, and short-chain acylcarnitines. The disruption of fatty acid, carbohydrate, and amino acid metabolism observed in the serum metabolome might be related to the previously observed impaired spermatogenesis in mice with early postnatal exposure to a low dose of BDE-209.

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“…Several tools are available for enrichment and overrepresentation analyses of metabolite data, such as, the MSEA (Metabolite Set Enrichment Analysis, http://www.msea.ca ) [ 58 ], which is now part of the MetaboAnalyst ( http://www.metaboanalyst.ca ); MBRole database (Metabolite Biological Role, http://csbg. cnb.csic.es/mbrole/ ) [ 59 ]; IMPaLA web-tool ( http://impala. molgen.mpg.de/ ) [ 60 ]; Consensus PathDB ( http://cpdb.molgen.mpg.de/ ) [ 61 ]; and the recently developed web-tool 3Omics ( http://3omics.cmdm.tw ) that is able to integrate transcriptomics, proteomics, and metabolomics data in a single platform [ 62 ].…”

Section: Notesmentioning

confidence: 99%

Xenobiotic Metabolism Activation as a Biomarker of Cigarette Smoke Exposure Response

Iskandar

2015

Methods in Pharmacology and Toxicology

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The recent advances in "omics" technologies have generated various in silico approaches for toxicity assessment. In silico-based toxicity predictions can overcome certain major drawbacks of laboratory experiments, including the limitation of conducting experiments in a chemical-by-chemical basis that can be expensive. This chapter discusses some recent applications of in silico approaches utilizing xenobiotic metabolism that can be used to assess the impact of cigarette smoke (CS). We fi rst outline recent studies using quantum mechanics/molecular modeling and quantitative structure-activity relationships that focus on smokingrelevant cytochrome P450 (CYP) enzymes. Subsequently, we describe several network-based approaches for toxicity assessment and relevant use cases leveraging a xenobiotic metabolism network model for a quantitative assessment of CS impact.

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MBRole: enrichment analysis of metabolomic data

Abstract: The web server is freely available at http://csbg.cnb.csic.es/mbrole. It was tested in the main web browsers.

Cited by 134 publications

References 10 publications

Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance (¹H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)

Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance (¹H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)

The effects of early postnatal exposure to a low dose of decabromodiphenyl ether (BDE-209) on serum metabolites in male mice

Xenobiotic Metabolism Activation as a Biomarker of Cigarette Smoke Exposure Response

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MBRole: enrichment analysis of metabolomic data

Abstract: The web server is freely available at http://csbg.cnb.csic.es/mbrole. It was tested in the main web browsers.

Cited by 134 publications

References 10 publications

Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance (1H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)

Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance (1H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)

The effects of early postnatal exposure to a low dose of decabromodiphenyl ether (BDE-209) on serum metabolites in male mice

Xenobiotic Metabolism Activation as a Biomarker of Cigarette Smoke Exposure Response

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Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance (¹H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)

Identification of endogenous metabolites in human sperm cells using proton nuclear magnetic resonance (¹H-NMR) spectroscopy and gas chromatography-mass spectrometry (GC-MS)