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Using MetaboAnalyst 3.0 for comprehensive metabolomics data analysis

Build and Broaden 3.0 AND Program Evaluation

Wishart DS, Xia J.
GSID: rR_FxJFuH-AJ
J Xia, DS Wishart - Current protocols in bioinformatics, 2016 - Wiley Online Library

Abstract MetaboAnalyst (http://www. metaboanalyst. ca) is a comprehensive Web application for metabolomic data analysis and interpretation. MetaboAnalyst handles most of the common metabolomic data types from most kinds of metabolomics platforms (MS and NMR) for most kinds of metabolomics...

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Xia, J., & Wishart, D. S. (2016). Using MetaboAnalyst 3.0 for comprehensive metabolomics data analysis. Current protocols in bioinformatics, 55(1), 14-10.
Xia, Jianguo, and David S. Wishart. "Using MetaboAnalyst 3.0 for comprehensive metabolomics data analysis." Current protocols in bioinformatics 55.1 (2016): 14-10.
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Boesenbergia rotunda: From Ethnomedicine to Drug Discovery.

Evidence-based complementary and alternative medicine : eCAM

Eng-Chong T, Yean-Kee L, Chin-Fei C, Choon-Han H, Sher-Ming W, Li-Ping CT, Gen-Teck F, Khalid N, Abd Rahman N, Karsani SA, Othman S, Othman R, Yusof R.
PMID: 23243448
Evid Based Complement Alternat Med. 2012;2012:473637. doi: 10.1155/2012/473637. Epub 2012 Nov 27.

Boesenbergia rotunda is a herb from the Boesenbergia genera under the Zingiberaceae family. B. rotunda is widely found in Asian countries where it is commonly used as a food ingredient and in ethnomedicinal preparations. The popularity of its ethnomedicinal...

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Eng-Chong T, Yean-Kee L, Chin-Fei C, et al. Boesenbergia rotunda: From Ethnomedicine to Drug Discovery. Evid Based Complement Alternat Med. 2012;2012:473637doi: 10.1155/2012/473637.
Eng-Chong, T., Yean-Kee, L., Chin-Fei, C., Choon-Han, H., Sher-Ming, W., Li-Ping, C. T., Gen-Teck, F., Khalid, N., Abd Rahman, N., Karsani, S. A., Othman, S., Othman, R., & Yusof, R. (2012). Boesenbergia rotunda: From Ethnomedicine to Drug Discovery. Evidence-based complementary and alternative medicine : eCAM, 2012473637. https://doi.org/10.1155/2012/473637
Eng-Chong, Tan, et al. "Boesenbergia rotunda: From Ethnomedicine to Drug Discovery." Evidence-based complementary and alternative medicine : eCAM vol. 2012 (2012): 473637. doi: https://doi.org/10.1155/2012/473637
Eng-Chong T, Yean-Kee L, Chin-Fei C, Choon-Han H, Sher-Ming W, Li-Ping CT, Gen-Teck F, Khalid N, Abd Rahman N, Karsani SA, Othman S, Othman R, Yusof R. Boesenbergia rotunda: From Ethnomedicine to Drug Discovery. Evid Based Complement Alternat Med. 2012;2012:473637. doi: 10.1155/2012/473637. Epub 2012 Nov 27. PMID: 23243448; PMCID: PMC3519102.
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Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer.

Oncoscience

Shim EH, Sudarshan S.
PMID: 26097881
Oncoscience. 2015 May 15;2(5):483-6. doi: 10.18632/oncoscience.165. eCollection 2015.

Alterations in metabolism are now considered a hallmark of cancer. One of the clearest links between metabolism and malignancy are oncometabolites. To date, several putative oncometabolites with transforming properties have been identified in the context of tumors due to...

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Shim EH, Sudarshan S. Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer. Oncoscience. 2015;2(5):483-6doi: 10.18632/oncoscience.165.
Shim, E. H., & Sudarshan, S. (2015). Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer. Oncoscience, 2(5), 483-6. https://doi.org/10.18632/oncoscience.165
Shim, Eun-Hee, and Sudarshan, Sunil. "Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer." Oncoscience vol. 2,5 (2015): 483-6. doi: https://doi.org/10.18632/oncoscience.165
Shim EH, Sudarshan S. Another small molecule in the oncometabolite mix: L-2-Hydroxyglutarate in kidney cancer. Oncoscience. 2015 May 15;2(5):483-6. doi: 10.18632/oncoscience.165. eCollection 2015. PMID: 26097881; PMCID: PMC4468334.
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Global Metabolomics Reveals the Metabolic Dysfunction in Ox-LDL Induced Macrophage-Derived Foam Cells.

Frontiers in pharmacology

Xu W, Wei Z, Dong J, Duan F, Chen K, Chen C, Liu J, Yang X, Chen L, Xiao H, Liu A.
PMID: 28912717
Front Pharmacol. 2017 Aug 31;8:586. doi: 10.3389/fphar.2017.00586. eCollection 2017.

Atherosclerosis (AS) is a chronic disorder of large arteries that is a major risk factors of high morbidity and mortality. Oxidative modification LDL is one of the important contributors to atherogenesis. Macrophages take up ox-LDL and convert into foam...

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Xu W, Wei Z, Dong J, et al. Global Metabolomics Reveals the Metabolic Dysfunction in Ox-LDL Induced Macrophage-Derived Foam Cells. Front Pharmacol. 2017;8:586doi: 10.3389/fphar.2017.00586.
Xu, W., Wei, Z., Dong, J., Duan, F., Chen, K., Chen, C., Liu, J., Yang, X., Chen, L., Xiao, H., & Liu, A. (2017). Global Metabolomics Reveals the Metabolic Dysfunction in Ox-LDL Induced Macrophage-Derived Foam Cells. Frontiers in pharmacology, 8586. https://doi.org/10.3389/fphar.2017.00586
Xu, Wenjuan, et al. "Global Metabolomics Reveals the Metabolic Dysfunction in Ox-LDL Induced Macrophage-Derived Foam Cells." Frontiers in pharmacology vol. 8 (2017): 586. doi: https://doi.org/10.3389/fphar.2017.00586
Xu W, Wei Z, Dong J, Duan F, Chen K, Chen C, Liu J, Yang X, Chen L, Xiao H, Liu A. Global Metabolomics Reveals the Metabolic Dysfunction in Ox-LDL Induced Macrophage-Derived Foam Cells. Front Pharmacol. 2017 Aug 31;8:586. doi: 10.3389/fphar.2017.00586. eCollection 2017. PMID: 28912717; PMCID: PMC5583968.
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Proteomic and metabolic traits of grape exocarp to explain different anthocyanin concentrations of the cultivars.

Frontiers in plant science

Negri AS, Prinsi B, Failla O, Scienza A, Espen L.
PMID: 26300900
Front Plant Sci. 2015 Aug 04;6:603. doi: 10.3389/fpls.2015.00603. eCollection 2015.

The role of grape berry skin as a protective barrier against damage by physical injuries and pathogen attacks requires a metabolism able to sustain biosynthetic activities such as those relating to secondary compounds (i.e., flavonoids). In order to draw...

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Negri AS, Prinsi B, Failla O, et al. Proteomic and metabolic traits of grape exocarp to explain different anthocyanin concentrations of the cultivars. Front Plant Sci. 2015;6:603doi: 10.3389/fpls.2015.00603.
Negri, A. S., Prinsi, B., Failla, O., Scienza, A., & Espen, L. (2015). Proteomic and metabolic traits of grape exocarp to explain different anthocyanin concentrations of the cultivars. Frontiers in plant science, 6603. https://doi.org/10.3389/fpls.2015.00603
Negri, Alfredo S, et al. "Proteomic and metabolic traits of grape exocarp to explain different anthocyanin concentrations of the cultivars." Frontiers in plant science vol. 6 (2015): 603. doi: https://doi.org/10.3389/fpls.2015.00603
Negri AS, Prinsi B, Failla O, Scienza A, Espen L. Proteomic and metabolic traits of grape exocarp to explain different anthocyanin concentrations of the cultivars. Front Plant Sci. 2015 Aug 04;6:603. doi: 10.3389/fpls.2015.00603. eCollection 2015. PMID: 26300900; PMCID: PMC4523781.
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Proton Nuclear Magnetic Resonance (NMR) Metabolomics: Future in Etiological Diagnosis of Encephalomyelitis.

Journal of neuroinfectious diseases

Sannagowdara K, Willoughby R, Whelan H.
PMID: 26339656
J Neuroinfect Dis. 2015 Aug;6(3). doi: 10.4172/2314-7326.1000184.

No abstract available.

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Sannagowdara K, Willoughby R, Whelan H. Proton Nuclear Magnetic Resonance (NMR) Metabolomics: Future in Etiological Diagnosis of Encephalomyelitis. J Neuroinfect Dis. 2015;6(3)doi: 10.4172/2314-7326.1000184.
Sannagowdara, K., Willoughby, R., & Whelan, H. (2015). Proton Nuclear Magnetic Resonance (NMR) Metabolomics: Future in Etiological Diagnosis of Encephalomyelitis. Journal of neuroinfectious diseases, 6(3), . https://doi.org/10.4172/2314-7326.1000184
Sannagowdara, Kumar, et al. "Proton Nuclear Magnetic Resonance (NMR) Metabolomics: Future in Etiological Diagnosis of Encephalomyelitis." Journal of neuroinfectious diseases vol. 6,3 (2015). doi: https://doi.org/10.4172/2314-7326.1000184
Sannagowdara K, Willoughby R, Whelan H. Proton Nuclear Magnetic Resonance (NMR) Metabolomics: Future in Etiological Diagnosis of Encephalomyelitis. J Neuroinfect Dis. 2015 Aug;6(3). doi: 10.4172/2314-7326.1000184. PMID: 26339656; PMCID: PMC4556357.
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Lipidomic Signature of Progression of Chronic Kidney Disease in the Chronic Renal Insufficiency Cohort.

Kidney international reports

Afshinnia F, Rajendiran TM, Karnovsky A, Soni T, Wang X, Xie D, Yang W, Shafi T, Weir MR, He J, Brecklin CS, Rhee EP, Schelling JR, Ojo A, Feldman H, Michailidis G, Pennathur S.
PMID: 28451650
Kidney Int Rep. 2016 Nov;1(4):256-268. doi: 10.1016/j.ekir.2016.08.007. Epub 2016 Aug 18.

INTRODUCTION: Human studies report conflicting results on the predictive power of serum lipids on progression of chronic kidney disease (CKD). We aimed to systematically identify the lipids that predict progression to end-stage kidney disease.METHODS: From the Chronic Renal Insufficiency...

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Afshinnia F, Rajendiran TM, Karnovsky A, et al. Lipidomic Signature of Progression of Chronic Kidney Disease in the Chronic Renal Insufficiency Cohort. Kidney Int Rep. 2016;1(4):256-268doi: 10.1016/j.ekir.2016.08.007.
Afshinnia, F., Rajendiran, T. M., Karnovsky, A., Soni, T., Wang, X., Xie, D., Yang, W., Shafi, T., Weir, M. R., He, J., Brecklin, C. S., Rhee, E. P., Schelling, J. R., Ojo, A., Feldman, H., Michailidis, G., & Pennathur, S. (2016). Lipidomic Signature of Progression of Chronic Kidney Disease in the Chronic Renal Insufficiency Cohort. Kidney international reports, 1(4), 256-268. https://doi.org/10.1016/j.ekir.2016.08.007
Afshinnia, Farsad, et al. "Lipidomic Signature of Progression of Chronic Kidney Disease in the Chronic Renal Insufficiency Cohort." Kidney international reports vol. 1,4 (2016): 256-268. doi: https://doi.org/10.1016/j.ekir.2016.08.007
Afshinnia F, Rajendiran TM, Karnovsky A, Soni T, Wang X, Xie D, Yang W, Shafi T, Weir MR, He J, Brecklin CS, Rhee EP, Schelling JR, Ojo A, Feldman H, Michailidis G, Pennathur S. Lipidomic Signature of Progression of Chronic Kidney Disease in the Chronic Renal Insufficiency Cohort. Kidney Int Rep. 2016 Nov;1(4):256-268. doi: 10.1016/j.ekir.2016.08.007. Epub 2016 Aug 18. PMID: 28451650; PMCID: PMC5402253.
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Rapid and noninvasive technique to assess the metabolomics profile of bovine embryos produced in vitro by Raman spectroscopy.

Biomedical optics express

Santos EC, Martinho HS, Annes K, Leite RF, Milazzotto MP.
PMID: 26309747
Biomed Opt Express. 2015 Jul 08;6(8):2830-9. doi: 10.1364/BOE.6.002830. eCollection 2015 Aug 01.

Morphological assessments are used to select embryos with the highest implantation potential, however it is still very limited. The development of new technologies, such as Raman spectroscopy have improved quantitative and qualitative analysis, and consequently led to a better...

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Santos EC, Martinho HS, Annes K, et al. Rapid and noninvasive technique to assess the metabolomics profile of bovine embryos produced in vitro by Raman spectroscopy. Biomed Opt Express. 2015;6(8):2830-9doi: 10.1364/BOE.6.002830.
Santos, E. C., Martinho, H. S., Annes, K., Leite, R. F., & Milazzotto, M. P. (2015). Rapid and noninvasive technique to assess the metabolomics profile of bovine embryos produced in vitro by Raman spectroscopy. Biomedical optics express, 6(8), 2830-9. https://doi.org/10.1364/BOE.6.002830
Santos, E C, et al. "Rapid and noninvasive technique to assess the metabolomics profile of bovine embryos produced in vitro by Raman spectroscopy." Biomedical optics express vol. 6,8 (2015): 2830-9. doi: https://doi.org/10.1364/BOE.6.002830
Santos EC, Martinho HS, Annes K, Leite RF, Milazzotto MP. Rapid and noninvasive technique to assess the metabolomics profile of bovine embryos produced in vitro by Raman spectroscopy. Biomed Opt Express. 2015 Jul 08;6(8):2830-9. doi: 10.1364/BOE.6.002830. eCollection 2015 Aug 01. PMID: 26309747; PMCID: PMC4541511.
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Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection.

Scientific reports

Feger BJ, Thompson JW, Dubois LG, Kommaddi RP, Foster MW, Mishra R, Shenoy SK, Shibata Y, Kidane YH, Moseley MA, Carnell LS, Bowles DE.
PMID: 27670941
Sci Rep. 2016 Sep 27;6:34091. doi: 10.1038/srep34091.

On Earth, biological systems have evolved in response to environmental stressors, interactions dictated by physical forces that include gravity. The absence of gravity is an extreme stressor and the impact of its absence on biological systems is ill-defined. Astronauts...

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Feger BJ, Thompson JW, Dubois LG, et al. Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection. Sci Rep. 2016;6:34091doi: 10.1038/srep34091.
Feger, B. J., Thompson, J. W., Dubois, L. G., Kommaddi, R. P., Foster, M. W., Mishra, R., Shenoy, S. K., Shibata, Y., Kidane, Y. H., Moseley, M. A., Carnell, L. S., & Bowles, D. E. (2016). Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection. Scientific reports, 634091. https://doi.org/10.1038/srep34091
Feger, Bryan J, et al. "Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection." Scientific reports vol. 6 (2016): 34091. doi: https://doi.org/10.1038/srep34091
Feger BJ, Thompson JW, Dubois LG, Kommaddi RP, Foster MW, Mishra R, Shenoy SK, Shibata Y, Kidane YH, Moseley MA, Carnell LS, Bowles DE. Microgravity induces proteomics changes involved in endoplasmic reticulum stress and mitochondrial protection. Sci Rep. 2016 Sep 27;6:34091. doi: 10.1038/srep34091. PMID: 27670941; PMCID: PMC5037457.
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Lipidomics of human umbilical cord serum: identification of unique sterol sulfates.

Future science OA

Wood PL, Siljander H, Knip M.
PMID: 28883994
Future Sci OA. 2017 Apr 05;3(3):FSO193. doi: 10.4155/fsoa-2017-0012. eCollection 2017 Aug.

AIM: There are currently limited lipidomics data for human umbilical cord blood. Therefore, the lipidomes of cord sera from six newborns and sera from six nonpregnant females were compared.MATERIALS & METHODS: Sera lipidomics analyses were conducted using a high-resolution...

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Wood PL, Siljander H, Knip M. Lipidomics of human umbilical cord serum: identification of unique sterol sulfates. Future Sci OA. 2017;3(3):FSO193doi: 10.4155/fsoa-2017-0012.
Wood, P. L., Siljander, H., & Knip, M. (2017). Lipidomics of human umbilical cord serum: identification of unique sterol sulfates. Future science OA, 3(3), FSO193. https://doi.org/10.4155/fsoa-2017-0012
Wood, Paul L, et al. "Lipidomics of human umbilical cord serum: identification of unique sterol sulfates." Future science OA vol. 3,3 (2017): FSO193. doi: https://doi.org/10.4155/fsoa-2017-0012
Wood PL, Siljander H, Knip M. Lipidomics of human umbilical cord serum: identification of unique sterol sulfates. Future Sci OA. 2017 Apr 05;3(3):FSO193. doi: 10.4155/fsoa-2017-0012. eCollection 2017 Aug. PMID: 28883994; PMCID: PMC5583693.
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Dietary and health biomarkers-time for an update.

Genes & nutrition

Dragsted LO, Gao Q, Praticò G, Manach C, Wishart DS, Scalbert A, Feskens EJM.
PMID: 28974991
Genes Nutr. 2017 Sep 29;12:24. doi: 10.1186/s12263-017-0578-y. eCollection 2017.

In the dietary and health research area, biomarkers are extensively used for multiple purposes. These include biomarkers of dietary intake and nutrient status, biomarkers used to measure the biological effects of specific dietary components, and biomarkers to assess the...

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Dragsted LO, Gao Q, Praticò G, et al. Dietary and health biomarkers-time for an update. Genes Nutr. 2017;12:24doi: 10.1186/s12263-017-0578-y.
Dragsted, L. O., Gao, Q., Praticò, G., Manach, C., Wishart, D. S., Scalbert, A., & Feskens, E. J. M. (2017). Dietary and health biomarkers-time for an update. Genes & nutrition, 1224. https://doi.org/10.1186/s12263-017-0578-y
Dragsted, Lars O, et al. "Dietary and health biomarkers-time for an update." Genes & nutrition vol. 12 (2017): 24. doi: https://doi.org/10.1186/s12263-017-0578-y
Dragsted LO, Gao Q, Praticò G, Manach C, Wishart DS, Scalbert A, Feskens EJM. Dietary and health biomarkers-time for an update. Genes Nutr. 2017 Sep 29;12:24. doi: 10.1186/s12263-017-0578-y. eCollection 2017. PMID: 28974991; PMCID: PMC5622518.
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Rice Bran and Probiotics Alter the Porcine Large Intestine and Serum Metabolomes for Protection against Human Rotavirus Diarrhea.

Frontiers in microbiology

Nealon NJ, Yuan L, Yang X, Ryan EP.
PMID: 28484432
Front Microbiol. 2017 Apr 21;8:653. doi: 10.3389/fmicb.2017.00653. eCollection 2017.

Human rotavirus (HRV) is a leading cause of severe childhood diarrhea, and there is limited vaccine efficacy in the developing world. Neonatal gnotobiotic pigs consuming a prophylactic synbiotic combination of probiotics and rice bran (Pro+RB) did not exhibit HRV...

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Nealon NJ, Yuan L, Yang X, et al. Rice Bran and Probiotics Alter the Porcine Large Intestine and Serum Metabolomes for Protection against Human Rotavirus Diarrhea. Front Microbiol. 2017;8:653doi: 10.3389/fmicb.2017.00653.
Nealon, N. J., Yuan, L., Yang, X., & Ryan, E. P. (2017). Rice Bran and Probiotics Alter the Porcine Large Intestine and Serum Metabolomes for Protection against Human Rotavirus Diarrhea. Frontiers in microbiology, 8653. https://doi.org/10.3389/fmicb.2017.00653
Nealon, Nora Jean, et al. "Rice Bran and Probiotics Alter the Porcine Large Intestine and Serum Metabolomes for Protection against Human Rotavirus Diarrhea." Frontiers in microbiology vol. 8 (2017): 653. doi: https://doi.org/10.3389/fmicb.2017.00653
Nealon NJ, Yuan L, Yang X, Ryan EP. Rice Bran and Probiotics Alter the Porcine Large Intestine and Serum Metabolomes for Protection against Human Rotavirus Diarrhea. Front Microbiol. 2017 Apr 21;8:653. doi: 10.3389/fmicb.2017.00653. eCollection 2017. PMID: 28484432; PMCID: PMC5399067.
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Showing 1 to 12 of 11401 entries