ArticleBioinformatics (Oxford, England)2019
Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 30 citations in OpenAlex.
- Article
- Emerging Urinary Biomarkers and Innovative Technologies for the Early Detection and Personalized Management of Chronic Kidney Disease.International journal of molecular sciences · 2026Review
- The Omics-Driven Machine Learning Path to Cost-Effective Precision Medicine in Chronic Kidney Disease.Proteomics · 2025Review
- DNEA: an R package for fast and versatile data-driven network analysis of metabolomics data.BMC bioinformatics · 2024Article
- ONDSA: a testing framework based on Gaussian graphical models for differential and similarity analysis of multiple omics networks.Briefings in bioinformatics · 2024Article
- Integrated multi-omics with machine learning to uncover the intricacies of kidney disease.Briefings in bioinformatics · 2024Review
- CorrelationCalculator and Filigree: Tools for Data-Driven Network Analysis of Metabolomics Data.Journal of visualized experiments : JoVE · 2023Article
- Body mass index associates with amyotrophic lateral sclerosis survival and metabolomic profiles.Muscle & nerve · 2023Article
- IntLIM 2.0: identifying multi-omic relationships dependent on discrete or continuous phenotypic measurements.Bioinformatics advances · 2023Article
- Metabolomics identifies shared lipid pathways in independent amyotrophic lateral sclerosis cohorts.Brain : a journal of neurology · 2022Article
- Present and future directions in diabetic kidney disease.Journal of diabetes and its complications · 2022Review
- Discovering a trans-omics biomarker signature that predisposes high risk diabetic patients to diabetic kidney disease.NPJ digital medicine · 2022Article
- Lipidomic profiling in the Strong Heart Study identified American Indians at risk of chronic kidney disease.Kidney international · 2022Article
- The Michigan O'Brien Kidney Research Center: transforming translational kidney research through systems biology.American journal of physiology. Renal physiology · 2022Review
- Transcriptomic data analysis coupled with copy number aberrations reveals a blood-based 17-gene signature for diagnosis and prognosis of patients with colorectal cancer.Frontiers in genetics · 2022Article
- Lipidomic approaches to dissect dysregulated lipid metabolism in kidney disease.Nature reviews. Nephrology · 2022Review
- Renin-angiotensin system inhibition reverses the altered triacylglycerol metabolic network in diabetic kidney disease.Metabolomics : Official journal of the Metabolomic Society · 2021Article
- Circulating short and medium chain fatty acids are associated with normoalbuminuria in type 1 diabetes of long duration.Scientific reports · 2021Article
- Lipidomics Reveals Serum Specific Lipid Alterations in Diabetic Nephropathy.Frontiers in endocrinology · 2021Article
- A Network-Based Methodology to Identify Subnetwork Markers for Diagnosis and Prognosis of Colorectal Cancer.Frontiers in genetics · 2021Article
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Authors and funding
17 authors at 13 institutions in 1 country.
Funding
Abstract
motivationFunctional enrichment testing methods can reduce data comprising hundreds of altered biomolecules to smaller sets of altered biological 'concepts' that help generate testable hypotheses. This study leveraged differential network enrichment analysis methodology to identify and validate lipid subnetworks that potentially differentiate chronic kidney disease (CKD) by severity or progression.
resultsWe built a partial correlation interaction network, identified highly connected network components, applied network-based gene-set analysis to identify differentially enriched subnetworks, and compared the subnetworks in patients with early-stage versus late-stage CKD. We identified two subnetworks 'triacylglycerols' and 'cardiolipins-phosphatidylethanolamines (CL-PE)' characterized by lower connectivity, and a higher abundance of longer polyunsaturated triacylglycerols in patients with severe CKD (stage ≥4) from the Clinical Phenotyping Resource and Biobank Core. These finding were replicated in an independent cohort, the Chronic Renal Insufficiency Cohort. Using an innovative method for elucidating biological alterations in lipid networks, we demonstrated alterations in triacylglycerols and cardiolipins-phosphatidylethanolamines that precede the clinical outcome of end-stage kidney disease by several years. AVAILABILITY AND IMPLEMENTATION: A complete list of NetGSA results in HTML format can be found at http://metscape.ncibi.org/netgsa/12345-022118/cric_cprobe/022118/results_cric_cprobe/main.html. The DNEA is freely available at https://github.com/wiggie/DNEA. Java wrapper leveraging the cytoscape.js framework is available at http://js.cytoscape.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.