Standardizing workflows in imaging transcriptomics with the abagen toolbox.
MRI
human
neuroimaging
neuroscience
processing variability
software
transcriptomics
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
16 11 2021
16 11 2021
Historique:
received:
12
07
2021
accepted:
15
11
2021
pubmed:
17
11
2021
medline:
22
1
2022
entrez:
16
11
2021
Statut:
epublish
Résumé
Gene expression fundamentally shapes the structural and functional architecture of the human brain. Open-access transcriptomic datasets like the Allen Human Brain Atlas provide an unprecedented ability to examine these mechanisms in vivo; however, a lack of standardization across research groups has given rise to myriad processing pipelines for using these data. Here, we develop the abagen toolbox, an open-access software package for working with transcriptomic data, and use it to examine how methodological variability influences the outcomes of research using the Allen Human Brain Atlas. Applying three prototypical analyses to the outputs of 750,000 unique processing pipelines, we find that choice of pipeline has a large impact on research findings, with parameters commonly varied in the literature influencing correlations between derived gene expression and other imaging phenotypes by as much as ρ ≥ 1.0. Our results further reveal an ordering of parameter importance, with processing steps that influence gene normalization yielding the greatest impact on downstream statistical inferences and conclusions. The presented work and the development of the abagen toolbox lay the foundation for more standardized and systematic research in imaging transcriptomics, and will help to advance future understanding of the influence of gene expression in the human brain.
Identifiants
pubmed: 34783653
doi: 10.7554/eLife.72129
pii: 72129
pmc: PMC8660024
doi:
pii:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIMH NIH HHS
ID : R01 MH083320
Pays : United States
Organisme : NIMH NIH HHS
ID : RF1 MH120021
Pays : United States
Organisme : NIBIB NIH HHS
ID : P41 EB019936
Pays : United States
Organisme : NIMH NIH HHS
ID : R01 MH096906
Pays : United States
Informations de copyright
© 2021, Markello et al.
Déclaration de conflit d'intérêts
RM, AA, JP, BF, AF, BM No competing interests declared
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