MarkerDB: an online database of molecular biomarkers

Wishart, David S.; Bartok, Brendan; Oler, Eponine; Liang, Kevin Y. H.; Budinski, Zachary; Berjanskii, Mark V.; Guo, Anchi; Cao, Xuan; Wilson, Michael

doi:10.1093/nar/gkaa1067

Cited by 77 publications

(78 citation statements)

References 24 publications

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“…Second, a proper statistical analysis was attempted, but it was only possible for the CRC and advanced adenoma vs. control and pre-surgery vs. post-surgery groups due to the need for a fold-change and a significant number of articles. For the compounds reported in each group, pathway enrichment was performed with different databases and meta-searches [ 52 , 53 , 54 , 55 ].…”

Section: Resultsmentioning

confidence: 99%

“…Inosine is involved in the degradation of purines for purine salvage, and its levels appear abnormal in urine in some metabolic and immune system disorders. Finally, adenosine is essential for life and is involved in many pathways, such as biological oxidation, signal transduction, and even energy transport, and its levels in urine appear altered in metabolic diseases and nervous system disorders [ 53 , 54 ].…”

Section: Discussionmentioning

confidence: 99%

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Comprehensive Volatilome and Metabolome Signatures of Colorectal Cancer in Urine: A Systematic Review and Meta-Analysis

Mallafré-Muro

Llambrich

Cumeras

et al. 2021

Cancers

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To increase compliance with colorectal cancer screening programs and to reduce the recommended screening age, cheaper and easy non-invasiveness alternatives to the fecal immunochemical test should be provided. Following the PRISMA procedure of studies that evaluated the metabolome and volatilome signatures of colorectal cancer in human urine samples, an exhaustive search in PubMed, Web of Science, and Scopus found 28 studies that met the required criteria. There were no restrictions on the query for the type of study, leading to not only colorectal cancer samples versus control comparison but also polyps versus control and prospective studies of surgical effects, CRC staging and comparisons of CRC with other cancers. With this systematic review, we identified up to 244 compounds in urine samples (3 shared compounds between the volatilome and metabolome), and 10 of them were relevant in more than three articles. In the meta-analysis, nine studies met the criteria for inclusion, and the results combining the case-control and the pre-/post-surgery groups, eleven compounds were found to be relevant. Four upregulated metabolites were identified, 3-hydroxybutyric acid, L-dopa, L-histidinol, and N1, N12-diacetylspermine and seven downregulated compounds were identified, pyruvic acid, hydroquinone, tartaric acid, and hippuric acid as metabolites and butyraldehyde, ether, and 1,1,6-trimethyl-1,2-dihydronaphthalene as volatiles.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Comprehensive Volatilome and Metabolome Signatures of Colorectal Cancer in Urine: A Systematic Review and Meta-Analysis

Mallafré-Muro

Llambrich

Cumeras

et al. 2021

Cancers

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“…This is because the presence and relative abundance of certain metabolites can serve as diagnostic indicators (biomarkers). Designation of several diagnostic metabolites has already allowed clinicians to confidently define health status, predict future disease risk, track disease progression, and chart the progress of various therapeutic interventions [ 18 ]. While metabolic signatures in blood and urine can non-invasively differentiate diseases, and may reflect various aspects of tissue-specific dysfunction and pathology, they are no substitute for directly measuring the diseased tissue.…”

Section: Introductionmentioning

confidence: 99%

Common Muscle Metabolic Signatures Highlight Arginine and Lysine Metabolism as Potential Therapeutic Targets to Combat Unhealthy Aging

Tokarz

Möller

Artati

et al. 2021

IJMS

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Biological aging research is expected to reveal modifiable molecular mechanisms that can be harnessed to slow or possibly reverse unhealthy trajectories. However, there is first an urgent need to define consensus molecular markers of healthy and unhealthy aging. Established aging hallmarks are all linked to metabolism, and a ‘rewired’ metabolic circuitry has been shown to accelerate or delay biological aging. To identify metabolic signatures distinguishing healthy from unhealthy aging trajectories, we performed nontargeted metabolomics on skeletal muscles from 2-month-old and 21-month-old mice, and after dietary and lifestyle interventions known to impact biological aging. We hypothesized that common metabolic signatures would highlight specific pathways and processes promoting healthy aging, while revealing the molecular underpinnings of unhealthy aging. Here, we report 50 metabolites that commonly distinguished aging trajectories in all cohorts, including 18 commonly reduced under unhealthy aging and 32 increased. We stratified these metabolites according to known relationships with various aging hallmarks and found the greatest associations with oxidative stress and nutrient sensing. Collectively, our data suggest interventions aimed at maintaining skeletal muscle arginine and lysine may be useful therapeutic strategies to minimize biological aging and maintain skeletal muscle health, function, and regenerative capacity in old age.

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“…Most of them focused on the protein (Wu et al, 2020), vocal (Sara et al, 2020), and imaging (Jivraj et al, 2017;Jose et al, 2020) data. So we collected the PH marker genes from the recently updated database MarkerDB (Wishart et al, 2021). Three unique genes were annotated as the PH biomarkers, including Bone Morphogenetic Protein Receptor Type 2 (BMPR2), Activin A Receptor Like Type 1 (ACVRL1), and Endoglin (ENG).…”

Section: Further Validation Of the Proposed Ph Biomarkersmentioning

confidence: 99%

EnRank: An Ensemble Method to Detect Pulmonary Hypertension Biomarkers Based on Feature Selection and Machine Learning Models

Liu¹,

Fu²,

Zhang³

et al. 2021

Front. Genet.

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Pulmonary hypertension (PH) is a common disease that affects the normal functioning of the human pulmonary arteries. The peripheral blood mononuclear cells (PMBCs) served as an ideal source for a minimally invasive disease diagnosis. This study hypothesized that the transcriptional fluctuations in the PMBCs exposed to the PH arteries may stably reflect the disease. However, the dimension of a human transcriptome is much higher than the number of samples in all the existing datasets. So, an ensemble feature selection algorithm, EnRank, was proposed to integrate the ranking information of four popular feature selection algorithms, i.e., T-test (Ttest), Chi-squared test (Chi2), ridge regression (Ridge), and Least Absolute Shrinkage and Selection Operator (Lasso). Our results suggested that the EnRank-detected biomarkers provided useful information from these four feature selection algorithms and achieved very good prediction accuracy in predicting the PH patients. Many of the EnRank-detected biomarkers were also supported by the literature.

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MarkerDB: an online database of molecular biomarkers

Cited by 77 publications

References 24 publications

Comprehensive Volatilome and Metabolome Signatures of Colorectal Cancer in Urine: A Systematic Review and Meta-Analysis

Comprehensive Volatilome and Metabolome Signatures of Colorectal Cancer in Urine: A Systematic Review and Meta-Analysis

Common Muscle Metabolic Signatures Highlight Arginine and Lysine Metabolism as Potential Therapeutic Targets to Combat Unhealthy Aging

EnRank: An Ensemble Method to Detect Pulmonary Hypertension Biomarkers Based on Feature Selection and Machine Learning Models

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