gene2gauss: A multi-view gaussian gene embedding learner for analyzing transcriptomic networks

AMIA Annu Symp Proc. 2022 May 23;2022:206-215. eCollection 2022.

Abstract

Analyzing gene co-expression networks can help in the discovery of biological processes and regulatory mechanisms underlying normal or perturbed states. Unlike standard differential analysis, network-based approaches consider the interactions between the genes involved leading to biologically relevant results. Applying such network-based methods to jointly analyze multiple transcriptomic networks representing independent disease cohorts or studies could lead to the identification of more robust gene modules or gene regulatory networks. We present gene2gauss, a novel feature learning framework that is capable of embedding genes as multivariate gaussian distributions by taking into account their long-range interaction neighborhoods across multiple transcriptomic studies. Using multiple gene co-expression networks from idiopathic pulmonary fibrosis, we demonstrate that these multi-dimensional gaussian features are suitable for identifying regulons of known transcription factors (TF). Using standard TF-target libraries, we demonstrate that the features from our method are highly relevant in comparison with other feature learning approaches on transcriptomic data.

MeSH terms

  • Gene Expression Profiling / methods
  • Gene Regulatory Networks*
  • Humans
  • Transcription Factors
  • Transcriptome*

Substances

  • Transcription Factors