Using machine learning to detect the differential usage of novel gene isoforms

Research output: Contribution to journalArticlepeer-review

Abstract

BACKGROUND: Differential isoform usage is an important driver of inter-individual phenotypic diversity and is linked to various diseases and traits. However, accurately detecting the differential usage of different gene transcripts between groups can be difficult, in particular in less well annotated genomes where the spectrum of transcript isoforms is largely unknown.

RESULTS: We investigated whether machine learning approaches can detect differential isoform usage based purely on the distribution of reads across a gene region. We illustrate that gradient boosting and elastic net approaches can successfully identify large numbers of genes showing potential differential isoform usage between Europeans and Africans, that are enriched among relevant biological pathways and significantly overlap those identified by previous approaches. We demonstrate that diversity at the 3' and 5' ends of genes are primary drivers of these differences between populations.

CONCLUSION: Machine learning methods can effectively detect differential isoform usage from read fraction data, and can provide novel insights into the biological differences between groups.

Original languageEnglish
Article number45
JournalBMC Bioinformatics
Volume23
Issue number1
Early online date18 Jan 2022
DOIs
Publication statusE-pub ahead of print - 18 Jan 2022

Keywords

  • Alternative Splicing
  • Exons
  • Gene Expression Profiling
  • Machine Learning
  • Protein Isoforms/genetics
  • Sequence Analysis, RNA

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