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Related Experiment Video

Updated: Oct 13, 2025

Mapping the Structure-Function Relationships of Disordered Oncogenic Transcription Factors Using Transcriptomic Analysis
09:58

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Published on: June 27, 2020

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Standardizing workflows in imaging transcriptomics with the abagen toolbox.

Ross D Markello1, Aurina Arnatkeviciute2, Jean-Baptiste Poline1

  • 1McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, Montreal, Canada.

Elife
|November 16, 2021
PubMed
Summary
This summary is machine-generated.

Processing choices significantly alter gene expression findings in brain atlases. The abagen toolbox aids standardization for reliable imaging transcriptomics research.

Keywords:
MRIhumanneuroimagingneuroscienceprocessing variabilitysoftwaretranscriptomics

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Area of Science:

  • Neuroscience
  • Genomics
  • Bioinformatics

Background:

  • Gene expression is crucial for human brain structure and function.
  • Open-access transcriptomic data, like the Allen Human Brain Atlas, enable in vivo studies.
  • Varied processing pipelines hinder standardized analysis of this data.

Purpose of the Study:

  • To develop the abagen toolbox for standardized transcriptomic data analysis.
  • To assess the impact of methodological variability on Allen Human Brain Atlas research outcomes.

Main Methods:

  • Developed the open-access abagen toolbox.
  • Applied 750,000 unique processing pipelines to transcriptomic data.
  • Conducted three prototypical analyses to evaluate methodological variability.

Main Results:

  • Processing pipeline choice significantly impacts research findings, altering gene expression-imaging phenotype correlations by up to ρ ≥ 1.0.
  • Gene normalization steps have the greatest influence on downstream statistical inferences.
  • Identified an ordering of parameter importance in data processing.

Conclusions:

  • Methodological variability in processing Allen Human Brain Atlas data substantially affects results.
  • The abagen toolbox promotes standardization in imaging transcriptomics.
  • This work advances understanding of gene expression's role in the human brain.