Bioinformatics method combined with logistic regression analysis reveal potentially important miRNAs in ischemic stroke

Biosci Rep. 2020 Aug 28;40(8):BSR20201154. doi: 10.1042/BSR20201154.

Abstract

Purpose: The present study aimed to investigate the comprehensive differential expression profile of microRNAs (miRNAs) by screening for miRNA expression in ischemic stroke and normal samples.

Methods: Differentially expressed miRNA (DEM) analysis was conducted using limma R Bioconductor package. Target genes of DEMs were identified from TargetScanHuman and miRTarBase databases. Functional enrichment analysis of the target genes was performed using clusterProfiler R Bioconductor package. The miRNA-based ischemic stroke diagnostic signature was constructed via logistic regression analysis.

Results: Compared with the normal cohort, a total of 14 DEMs, including 5 up-regulated miRNAs and 9 down-regulated miRNAs, were identified in ischemic stroke patients. These DEMs have 1600 regulatory targets. Using a logistic regression model, the top five miRNAs were screened for constructing an miRNA-based ischemic stroke diagnostic signature. Using the miRNA-mRNA interaction pairs, two target genes (specificity protein 1 (SP1) and Argonaute 1 (AGO1)) were speculated to be the primary genes of ischemic stroke.

Discussion and conclusion: Here, several potential miRNAs biomarkers were identified and an miRNA-based diagnostic signature for ischemic stroke was established, which can be a valuable reference for future clinical researches.

Keywords: ischemic stroke; machine learning algorithms; miRNAs.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Argonaute Proteins / genetics
  • Case-Control Studies
  • Computational Biology*
  • Databases, Genetic
  • Eukaryotic Initiation Factors / genetics
  • Gene Expression Profiling*
  • Gene Regulatory Networks
  • Humans
  • Ischemic Stroke / diagnosis*
  • Ischemic Stroke / genetics
  • Logistic Models
  • Machine Learning
  • MicroRNAs / genetics*
  • Predictive Value of Tests
  • Risk Assessment
  • Risk Factors
  • Sp1 Transcription Factor / genetics
  • Transcriptome*

Substances

  • AGO1 protein, human
  • Argonaute Proteins
  • Eukaryotic Initiation Factors
  • MicroRNAs
  • Sp1 Transcription Factor
  • SP1 protein, human