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Regional juxtacortical microstructural changes and gene expression provide insights into neurodegeneration in Alzheimer's disease.

Code ↔ Paper

2 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 2 matches
  1. [1] § Results › Relating FWF changes to variation in gene expression patterns in AD ↔ Analysis of AD-related gene from Genecards.py, lines 11–21 · score 0.76 · AD related genes, GeneCards, relevance score, genes overlapped, background genes, PLS1
  2. [2] § Methods › Analysis of AD-related genes from GeneCards gene database ↔ Analysis of AD-related gene from Genecards.py, lines 11–21 · score 0.75 · AD related genes, GeneCards, relevance score, background genes, overlapped

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

Python · 41 lines · 1.1 KB · no license · 2 matches

  2. import pandas as pd
  3. from scipy.stats import pearsonr
  5. # Background gene
  6. df1 = pd.read_excel(path+'expression_L.xlsx')
  8. # PLS1 significant genes
  9. df2 = pd.read_excel(path+'PLS_res.xlsx')
  11. # AD-related genes from GeneCards
  12. df3 = pd.read_csv(path+'GeneCards-SearchResults.csv')
  13. df3 = df3[df3['Relevance score']>7]
  15. bgge = df1.columns
  16. opge0 = list( set(bgge)&set(list(df3['Gene Symbol'])) )
  17. opge = list( set(opge0)&set(list(df2['Genes'])) )
  19. print("-Number of genes overlapping with background genes：",len(opge0))
  20. print('-Number of genes overlapping with PLS1 significant genes',len(opge))
  21. print(df2[df2['Genes'].isin(opge)])
  23. # t-map correlation analysis
  24. df4 = pd.read_excel(path+'t_map_pval.xlsx')
  25. t_stats = list(df4['t_stats'])
  26. t_stats = t_stats[0:41]
  28. exp_opge = df1[opge]
  29. corr_res = pd.DataFrame()
  30. ps=[];cors=[]
  31. for ge in opge:
  32. corr, p_value = pearsonr(exp_opge[ge], t_stats)
  33. ps.append(p_value)
  34. cors.append(corr)
  36. corr_res['Genes'] = opge
  37. corr_res['Correlation'] = cors
  38. corr_res['p-value'] = ps
  39. corr_res = corr_res.sort_values(by='Correlation')
  40. print(corr_res)

Analysis of AD-related gene from Genecards.py at commit cd661bb, no license · at the source

Overview

Authors: Junfang Zhang1,2, Lipeng Sun2,3, Xinyuan Yang2,3, Lin Kang2,3, Yingting Zheng2, Qi Huang4, Wei Xu2, Yihui Guan4, Jun Liu2,3, Yulei Deng2,3, Fang Xie4, Xiaomeng Xu2,3, Binyin Li5
ORCID iDs: Junfang Zhang, Fang Xie, Xiaomeng Xu, Binyin Li
  1. Department of Neurology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
  2. Department of Neurology & Institute of Neurology, Ruijin Hospital affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
  3. Clinical Neuroscience Center, Ruijin Hospital LuWan Branch, Shanghai Jiao Tong University School of Medicine, Shanghai, China
  4. Department of Nuclear Medicine & PET Center, Huashan Hospital, Fudan University, Shanghai, China
  5. Neurology, Taicang Loujiang New City Hospital (Ruijin Hospital, Taicang), Taicang, China, Shanghai, China
Institutions: Shanghai Jiao Tong University (China); Ruijin Hospital (China); Shanghai Sixth People's Hospital (China); Fudan University (China); Huashan Hospital (China)
Journal: Translational psychiatry, volume 16, issue 1, article 469
Dates: received 8 February 2026; accepted 15 July 2026; published online 30 July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41398-026-04292-z · PMID 42744775 · PMCID PMC13578702 · OpenAlex W7171764663
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), structural MRI / diffusion (modality), PET / SPECT (modality), human (organism), Alzheimer's / dementia (population), cellular / molecular (subfield)
Methods: Statistics, Preprocessing, Connectivity, fMRI & imaging, Smoothing, state filtering, decompositions
Keywords: Molecular neuroscience, Clinical genetics
MeSH: Alzheimer Disease*, Gene Expression*, White Matter*, Aged, Aged, 80 and over, Diffusion Magnetic Resonance Imaging, Female, Humans, Male, Positron-Emission Tomography, Transcriptome (* major topic)
Topic: Alzheimer's disease research and treatments (Physiology, Medicine), according to OpenAlex
Funding: Alzheimer's Disease Neuroimaging Initiative; National Natural Science Foundation of China (82271441, 2022ZD0213800, 82571604); National Key Research and Development Program of China (2022ZD0213800); Fundamental Research Funds for the Central Universities (YG2025QNA45)
Citations: not cited yet (Europe PMC); 54 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 2 matches between paragraphs and lines of code.

Sahuhu-Sun/Imaging-transcriptomics

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: cd661bbfc3b58ec31500e08e2ac36b4291cb516c, 19 October 2025
Languages: Python (3), R (1)
Size: 5 files, 4 scripts
Software Heritage: not archived
Found in: “Data availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: pandas (3 files), NumPy (2 files), SciPy (2 files), statsmodels (2 files), ggplot2 (1 file), scikit-learn (1 file), tidyverse (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
5 files
At the source: github.com/Sahuhu-Sun/Imaging-transcriptomics

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 4 scripts, each with its path and the digest of its content;
  • 2 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

Code and data availability statement

The paper has a code and data availability statement. Its license (CC BY-NC-ND) does not allow reproducing it here; in short, from what the harvester recognized in it:

Read it in the paper: doi.org/10.1038/s41398-026-04292-z.

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 2, 28 September 2026

  • Funding: added Alzheimer's Disease Neuroimaging Initiative; National Natural Science Foundation of China: 82271441, 2022ZD0213800, 82571604; National Key Research and Development Program of China: 2022ZD0213800; Fundamental Research Funds for the Central Universities: YG2025QNA45

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 13 authors, 2 keywords, 11 MeSH terms, 54 references.

Cite

This paper

Zhang, J., Sun, L., Yang, X., Kang, L., Zheng, Y., Huang, Q., Xu, W., Guan, Y., Liu, J., Deng, Y., Xie, F., Xu, X., & Li, B. (2026). Regional juxtacortical microstructural changes and gene expression provide insights into neurodegeneration in Alzheimer's disease. Translational psychiatry, 16(1), 469. https://doi.org/10.1038/s41398-026-04292-z

BibTeX

@article{zhang2026regional,
author = {Zhang, Junfang and Sun, Lipeng and Yang, Xinyuan and Kang, Lin and Zheng, Yingting and Huang, Qi and Xu, Wei and Guan, Yihui and Liu, Jun and Deng, Yulei and Xie, Fang and Xu, Xiaomeng and Li, Binyin},
title = {{Regional juxtacortical microstructural changes and gene expression provide insights into neurodegeneration in Alzheimer's disease}},
journal = {Translational psychiatry},
year = {2026},
month = jul,
volume = {16},
number = {1},
pages = {469},
publisher = {Nature Publishing Group},
issn = {2158-3188},
doi = {10.1038/s41398-026-04292-z},
url = {https://doi.org/10.1038/s41398-026-04292-z},
pmid = {42744775},
pmcid = {PMC13578702}
}

RIS

TY - JOUR
AU - Zhang, Junfang
AU - Sun, Lipeng
AU - Yang, Xinyuan
AU - Kang, Lin
AU - Zheng, Yingting
AU - Huang, Qi
AU - Xu, Wei
AU - Guan, Yihui
AU - Liu, Jun
AU - Deng, Yulei
AU - Xie, Fang
AU - Xu, Xiaomeng
AU - Li, Binyin
TI - Regional juxtacortical microstructural changes and gene expression provide insights into neurodegeneration in Alzheimer's disease
T2 - Translational psychiatry
J2 - Transl Psychiatry
PY - 2026
DA - 2026/07/30
VL - 16
IS - 1
SP - 469
SN - 2158-3188
PB - Nature Publishing Group
DO - 10.1038/s41398-026-04292-z
UR - https://doi.org/10.1038/s41398-026-04292-z
LA - en
ER -

CSL-JSON

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