Systematic Evaluation of Competing Brain Transcriptomic Representations Reveals Reciprocal Patterns Across Heterogeneous Contexts.
Overview
Abstract
Adaptive and adverse brain states are often assumed to lie on a shared molecular continuum, but this assumption has rarely been evaluated against explicit transcriptomic alternatives. This study aimed to compare two representations of cross-context brain transcriptomic organization: a transcriptome-wide global-axis model and a low-dimensional reciprocal model. We benchmarked these models across a curated cross-study brain cohort spanning exercise, alcohol-related adversity-like contexts, stress, aging, and neurodegeneration, using prespecified intervention-like and adversity-like directional contrast labels rather than assuming homogeneous biological states. We assessed the competing representations using signed-effect correlations, permutation analyses, non-linear fitting, and held-out reconstruction, and we then examined the resulting structure through region-specific human bulk evaluation and exploratory cellular, single-nucleus, spatial, and chromatin projection analyses. These downstream analyses were used to examine localization and biological interpretability and were not treated as independent evaluation of the module 1/
Reproduced under the paper's license (CC BY), from the paper cited above.
Code
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Data
Datasets cited
- geo:GSE111212, at NCBI GEO; found in the references
Data Availability Statement
The public accessions used for primary discovery, human evaluation, cellular localization, spatial analysis, and chromatin projection are listed in Table 1. The 21 unique GEO accessions that contributed directly to this study are available from the NCBI Gene Expression Omnibus (GEO). Direct GEO record links for all accessions are provided in accession-and-URL format below. All URLs were accessed on 3 April 2026: GSE299436 (https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 7 keywords, 4 MeSH terms, 60 references.
Cite
This paper
Lyu, Z., Shao, C., Yu, Q., Yang, R., Yang, G., & Wang, Z. (2026). Systematic Evaluation of Competing Brain Transcriptomic Representations Reveals Reciprocal Patterns Across Heterogeneous Contexts. International journal of molecular sciences, 27(13), 6083. https://
BibTeX
@article{lyu2026systemat
author = {Lyu, Zongnan and Shao, Chunxue and Yu, Qi and Yang, Renyu and Yang, Guang and Wang, Ziheng},
title = {{Systematic Evaluation of Competing Brain Transcriptomic Representations Reveals Reciprocal Patterns Across Heterogeneous Contexts}},
journal = {International journal of molecular sciences},
year = {2026},
month = jul,
volume = {27},
number = {13},
pages = {6083},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
issn = {1422-0067},
doi = {10.3390/
url = {https://
pmid = {42450348},
pmcid = {PMC13362261}
}
RIS
TY - JOUR
AU - Lyu, Zongnan
AU - Shao, Chunxue
AU - Yu, Qi
AU - Yang, Renyu
AU - Yang, Guang
AU - Wang, Ziheng
TI - Systematic Evaluation of Competing Brain Transcriptomic Representations Reveals Reciprocal Patterns Across Heterogeneous Contexts
T2 - International journal of molecular sciences
J2 - Int J Mol Sci
PY - 2026
DA - 2026/
VL - 27
IS - 13
SP - 6083
SN - 1422-0067
PB - Multidisciplinary Digital Publishing Institute (MDPI)
DO - 10.3390/
UR - https://
LA - en
ER -
CSL-JSON
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"container-title": "International journal of molecular sciences",
"author": [
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"given": "Ziheng"
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"volume": "27",
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"DOI": "10.3390/
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"ISSN": "1422-0067",
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"URL": "https://
"language": "en",
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