Triclustering method for finding biomarkers in human immunodeficiency virus-1 gene expression data

Titin Siswantining, Alhadi Bustamam, Devvi Sarwinda, Saskya Mary Soemartojo, Moh Abdul Latief, Elke Annisa Octaria, Anggrainy Togi Marito Siregar, Oon Septa, Herley Shaori Al-Ash, Noval Saputra

Research output: Contribution to journalArticlepeer-review

Abstract

HIV-1 is a virus that destroys CD4 + cells in the body's immune system, causing a drastic decline in immune system performance. Analysis of HIV-1 gene expression data is urgently needed. Microarray technology is used to analyze gene expression data by measuring the expression of thousands of genes in various conditions. The gene expression series data, which are formed in three dimensions, are analyzed using triclustering. Triclustering is an analysis technique for 3D data that aims to group data simultaneously into rows and columns across different times/conditions. The result of this technique is called a tricluster. A tricluster is a subspace in the form of a subset of rows, columns, and time/conditions. In this study, we used the δ-Trimax, THD Tricluster, and MOEA methods by applying different measures, namely, transposed virtual error, the New Residue Score, and the Multi Slope Measure. The gene expression data consisted of 22,283 probe gene IDs, 40 observations, and four conditions: normal, acute, chronic, and non-progressor. Tricluster evaluation was carried out based on intertemporal homogeneity. An analysis of the probe ID gene that affects AIDS was carried out through this triclustering process. Based on this analysis, a gene symbol which is biomarkers associated with AIDS due to HIV-1, HLA-C, was found in every condition for normal, acute, chronic, and non-progressive HIV-1 patients.

Original languageEnglish
Pages (from-to)6743-6763
Number of pages21
JournalMathematical Biosciences and Engineering
Volume19
Issue number7
DOIs
Publication statusPublished - 2022

Keywords

  • biclustering
  • genetic based
  • multi slope measure
  • thd-tricluster
  • transposed virtual error

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