Application of Sparse Linear Discriminant Analysis and Elastic Net for Diagnosis of IgA Nephropathy: Statistical and Biological Viewpoints

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MOHAMMADI MAJD TAHEREH; KALANTARI SHIVA; Raeisi Shahraki Hadi; NAFAR MOHSEN; ALMASI AFSHIN; SAMAVAT SHIVA; PARVIN MAHMOUD; HASHEMIAN AMIR HOSSEIN

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Journal: Iranian Biomedical Journal Year:2018 | Volume:22 | Issue:6 Page(s): 374-384

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Title

Application of Sparse Linear Discriminant Analysis and Elastic Net for Diagnosis of IgA Nephropathy: Statistical and Biological Viewpoints

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Keywords

Biomarker

Diagnosis

IgA nephropathy

Proteomics

Abstract

Background: IgA nephropathy (IgAN) is the most common primary glomerulonephritis diagnosed based on renal biopsy. Mesangial IgA deposits along with the proliferation of mesangial cells are the histologic hallmark of IgAN. Non-invasive diagnostic tools may help to prompt Diagnosis and therapy. The discovery of potential and reliable urinary Biomarkers for Diagnosis of IgAN depends on applying robust and suitable models. Applying two multivariate modeling methods on a urine proteomic dataset were obtained from IgAN patients, and comparison of the results of these methods were the purpose of this study. Methods: Two models were constructed for urinary protein profiles of 13 patients and 8 healthy individuals, based on sparse linear discriminant analysis (SLDA) and elastic net (EN) regression methods. A panel of selected Biomarkers with the best coefficients were proposed and further analyzed for biological relevance using functional annotation and pathway analysis. Results: Transferrin, α 1-antitrypsin, and albumin fragments were the most important up-regulated Biomarkers, while fibulin-5, YIP1 family member 3, prasoposin, and osteopontin were the most important down-regulated Biomarkers. Pathway analysis revealed that complement and coagulation cascades and extracellular matrix-receptor interaction pathways impaired in the pathogenesis of IgAN. Conclusion: SLDA and EN had an equal importance for Diagnosis of IgAN and were useful methods for exploring and processing proteomic data. In addition, the suggested Biomarkers are reliable candidates for further validation to non-invasive diagnose of IgAN based on urine examination.

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APA: Copy

MOHAMMADI MAJD, TAHEREH, KALANTARI, SHIVA, Raeisi Shahraki, Hadi, NAFAR, MOHSEN, ALMASI, AFSHIN, SAMAVAT, SHIVA, PARVIN, MAHMOUD, & HASHEMIAN, AMIR HOSSEIN. (2018). Application of Sparse Linear Discriminant Analysis and Elastic Net for Diagnosis of IgA Nephropathy: Statistical and Biological Viewpoints. IRANIAN BIOMEDICAL JOURNAL, 22(6), 374-384. SID. https://sid.ir/paper/756418/en

Vancouver: Copy

MOHAMMADI MAJD TAHEREH, KALANTARI SHIVA, Raeisi Shahraki Hadi, NAFAR MOHSEN, ALMASI AFSHIN, SAMAVAT SHIVA, PARVIN MAHMOUD, HASHEMIAN AMIR HOSSEIN. Application of Sparse Linear Discriminant Analysis and Elastic Net for Diagnosis of IgA Nephropathy: Statistical and Biological Viewpoints. IRANIAN BIOMEDICAL JOURNAL[Internet]. 2018;22(6):374-384. Available from: https://sid.ir/paper/756418/en

IEEE: Copy

TAHEREH MOHAMMADI MAJD, SHIVA KALANTARI, Hadi Raeisi Shahraki, MOHSEN NAFAR, AFSHIN ALMASI, SHIVA SAMAVAT, MAHMOUD PARVIN, and AMIR HOSSEIN HASHEMIAN, “Application of Sparse Linear Discriminant Analysis and Elastic Net for Diagnosis of IgA Nephropathy: Statistical and Biological Viewpoints,” IRANIAN BIOMEDICAL JOURNAL, vol. 22, no. 6, pp. 374–384, 2018, [Online]. Available: https://sid.ir/paper/756418/en

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