Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease

Jing Ma, Alla Karnovsky, Farsad Afshinnia, Janis Wigginton, Daniel J. Rader, Loki Natarajan, Kumar Sharma, Anna C. Porter, Mahboob Rahman, Jiang He, Lee Hamm, Tariq Shafi, Debbie Gipson, Crystal Gadegbeku, Harold Feldman, George Michailidis, Subramaniam Pennathur

Research output: Contribution to journalArticle

Abstract

MOTIVATION: Functional 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. RESULTS: We 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.

Original languageEnglish (US)
Pages (from-to)3441-3452
Number of pages12
JournalBioinformatics (Oxford, England)
Volume35
Issue number18
DOIs
StatePublished - Sep 15 2019

Fingerprint

Kidney
Lipids
Chronic Renal Insufficiency
Pathway
Phosphatidylethanolamines
Triglycerides
Cardiolipins
Network components
HTML
Gene Regulatory Networks
Biomolecules
Partial Correlation
Bioinformatics
Computational Biology
Wrapper
Chronic Kidney Failure
Differentiate
Progression
Genes
Availability

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Ma, J., Karnovsky, A., Afshinnia, F., Wigginton, J., Rader, D. J., Natarajan, L., ... Pennathur, S. (2019). Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease. Bioinformatics (Oxford, England), 35(18), 3441-3452. https://doi.org/10.1093/bioinformatics/btz114

Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease. / Ma, Jing; Karnovsky, Alla; Afshinnia, Farsad; Wigginton, Janis; Rader, Daniel J.; Natarajan, Loki; Sharma, Kumar; Porter, Anna C.; Rahman, Mahboob; He, Jiang; Hamm, Lee; Shafi, Tariq; Gipson, Debbie; Gadegbeku, Crystal; Feldman, Harold; Michailidis, George; Pennathur, Subramaniam.

In: Bioinformatics (Oxford, England), Vol. 35, No. 18, 15.09.2019, p. 3441-3452.

Research output: Contribution to journalArticle

Ma, J, Karnovsky, A, Afshinnia, F, Wigginton, J, Rader, DJ, Natarajan, L, Sharma, K, Porter, AC, Rahman, M, He, J, Hamm, L, Shafi, T, Gipson, D, Gadegbeku, C, Feldman, H, Michailidis, G & Pennathur, S 2019, 'Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease', Bioinformatics (Oxford, England), vol. 35, no. 18, pp. 3441-3452. https://doi.org/10.1093/bioinformatics/btz114
Ma, Jing ; Karnovsky, Alla ; Afshinnia, Farsad ; Wigginton, Janis ; Rader, Daniel J. ; Natarajan, Loki ; Sharma, Kumar ; Porter, Anna C. ; Rahman, Mahboob ; He, Jiang ; Hamm, Lee ; Shafi, Tariq ; Gipson, Debbie ; Gadegbeku, Crystal ; Feldman, Harold ; Michailidis, George ; Pennathur, Subramaniam. / Differential network enrichment analysis reveals novel lipid pathways in chronic kidney disease. In: Bioinformatics (Oxford, England). 2019 ; Vol. 35, No. 18. pp. 3441-3452.
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