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The proteomic and metabolomic signature of inherited chromosomally integrated HHV-6 and its role in all-cause dementia and mortality risk: The UK Biobank study.

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Paper

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The authors' code

R · 65 lines · 2.7 KB · no license

  1. # Load necessary libraries
  2. library(ggplot2)
  3. library(dplyr)
  4. library(ggrepel)
  6. # Set working directory
  7. setwd("E://16GBBACKUPUSB//BACKUP_USB_SEPTEMBER2014//May Baydoun_folder//UK_BIOBANK_PROJECT//UKB_PAPER25_HHV6_DEM_AD_PROT_METAB//MANUSCRIPT//GITHUB//FIGURES//FIGURE3//FIGURE3A//")
  9. # Load datasets
  10. list_metabolites <- read.csv("List_METABOLITES.csv", stringsAsFactors = FALSE)
  11. regression_results <- read.csv("Supplementary_datasheet1.csv", stringsAsFactors = FALSE)
  13. # Ensure 'Fieldnum' exists in both datasets
  14. if(!all(c("Fieldnum") %in% colnames(list_metabolites)) ||
  15. !all(c("Fieldnum") %in% colnames(regression_results))) {
  16. stop("Fieldnum column missing from one of the datasets.")
  17. }
  19. # Merge datasets
  20. merged_data <- merge(regression_results, list_metabolites, by = "Fieldnum")
  22. # Check for required columns
  23. required_cols <- c("estimate", "p", "Abbreviation")
  24. if(!all(required_cols %in% colnames(merged_data))) {
  25. stop(paste("Missing required columns:", paste(setdiff(required_cols, colnames(merged_data)), collapse = ", ")))
  26. }
  28. # Transform and annotate
  29. merged_data <- merged_data %>%
  30. mutate(log10p = -log10(p),
  31. label = ifelse(estimate > 0.04 | estimate < -0.04, Abbreviation, NA),
  32. color_group = case_when(
  33. estimate > 0.04 ~ "High",
  34. estimate < -0.04 ~ "Low",
  35. TRUE ~ "Neutral"
  36. ))
  38. # Bonferroni and type I error cutoffs
  39. bonferroni_cutoff <- -log10(0.05 / 249)
  40. typeIerror_cutoff <- -log10(0.05)
  41. max_y <- max(merged_data$log10p, na.rm = TRUE)
  43. # Volcano plot
  44. volcano_plot <- ggplot(merged_data, aes(x = estimate, y = log10p)) +
  45. geom_point(aes(color = color_group), alpha = 0.7) +
  46. geom_hline(yintercept = bonferroni_cutoff, linetype = "dashed", color = "grey") +
  47. geom_hline(yintercept = typeIerror_cutoff, linetype = "dashed", color = "black") +
  48. geom_vline(xintercept = c(-0.04, 0.04), linetype = "dashed", color = "blue") +
  49. geom_text_repel(aes(label = label), size = 3, na.rm = TRUE, max.overlaps = Inf,
  50. box.padding = 0.5, point.padding = 0.5, force = 5, segment.size = 0.2) +
  51. scale_x_continuous(breaks = c(-0.10, -0.07, -0.05, 0, 0.05, 0.07, 0.10, 0.15),
  52. limits = c(-0.10, 0.15)) +
  53. scale_y_continuous(limits = c(0, max_y * 1.2)) +
  54. scale_color_manual(values = c("High" = "red", "Low" = "blue", "Neutral" = "black")) +
  55. theme_classic() +
  56. labs(title = "Volcano Plot of ici-HHV6 vs. metabolites",
  57. x = "Estimate",
  58. y = "-log10(p-value)") +
  59. theme(plot.title = element_text(hjust = 0.5))
  61. # Save plot
  62. ggsave("Figure3A.jpeg", plot = volcano_plot, device = "jpeg", width = 7, height = 5, dpi = 300)
  64. # Print to screen
  65. print(volcano_plot)

Figure3A.R at commit bbd73a9, no license · at the source

Overview

Authors: May A. Beydoun1, Minkyo Song1, Choa Yun1, Nicole Noren Hooten1, Jordan Weiss2, Hind A. Beydoun3,4, Michael R. Duggan5, Keenan A. Walker5, Lenore J. Launer1, Michele K. Evans1, Alan B. Zonderman1
  1. Laboratory of Epidemiology and Population Sciences National Institute on Aging, NIA/NIH/IRP Baltimore Maryland USA
  2. Optimal Aging Institute New York University Grossman School of Medicine New York New York USA
  3. VA National Center on Homelessness Among Veterans U.S. Department of Veterans Affairs Washington District of Columbia USA
  4. Department of Management, Policy, and Community Health, School of Public Health University of Texas Health Science Center at Houston Houston Texas USA
  5. Laboratory of Behavioral Neuroscience National Institute on Aging, NIA/NIH/IRP Baltimore Maryland USA
Institutions: National Institutes of Health (United States); National Institute on Aging (United States); New York University (United States); United States Department of Veterans Affairs (United States); The University of Texas Health Science Center at Houston (United States)
Journal: Alzheimer's & dementia (New York, N. Y.), volume 12, issue 3, article e70286
Dates: received 16 March 2026; accepted 7 June 2026; published online 20 July 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1002/trc2.70286 · PMID 42483205 · PMCID PMC13385209 · OpenAlex W7169876525
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), human (organism), Alzheimer's / dementia (population), clinical / translational (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning
Keywords: aging, dementia, iciHHV‐6, metabolome, mortality, proteome
Topic: Cytomegalovirus and herpesvirus research (Epidemiology, Medicine), according to OpenAlex
Funding: Intramural Research Program of the NIH; U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging); NIH (AG000513, AG000522)
Citations: not cited yet (Europe PMC); 50 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.

baydounm/UKB-paper25-supplementarydata

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: bbd73a98ab8280cbc0f755c480b75ef6cea216ad, 13 April 2026
Languages: R (2)
Size: 97 files, 2 scripts
Software Heritage: not archived
Found in: “CODE AVAILABILITY”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: ggplot2 (2 files), tidyverse (2 files)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
3 files
At the source: github.com/baydounm/UKB-paper25-supplementarydata

Code availability statement

The paper has a code 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/10.1002/trc2.70286.

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;
  • 2 scripts, each with its path and the digest of its content;
  • no match between paragraphs and code yet;
  • 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

Data availability statement

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

  • no repository, dataset or request procedure was recognized in it

Read it in the paper: doi.org/10.1002/trc2.70286.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 6 keywords, 3 funders, 50 references.

Cite

This paper

Beydoun, M. A., Song, M., Yun, C., Noren Hooten, N., Weiss, J., Beydoun, H. A., Duggan, M. R., Walker, K. A., Launer, L. J., Evans, M. K., & Zonderman, A. B. (2026). The proteomic and metabolomic signature of inherited chromosomally integrated HHV-6 and its role in all-cause dementia and mortality risk: The UK Biobank study. Alzheimer's & dementia (New York, N. Y.), 12(3), e70286. https://doi.org/10.1002/trc2.70286

BibTeX

@article{beydoun2026proteomic,
author = {Beydoun, May A. and Song, Minkyo and Yun, Choa and Noren Hooten, Nicole and Weiss, Jordan and Beydoun, Hind A. and Duggan, Michael R. and Walker, Keenan A. and Launer, Lenore J. and Evans, Michele K. and Zonderman, Alan B.},
title = {{The proteomic and metabolomic signature of inherited chromosomally integrated HHV-6 and its role in all-cause dementia and mortality risk: The UK Biobank study}},
journal = {Alzheimer's \& dementia (New York, N. Y.)},
year = {2026},
month = jul,
volume = {12},
number = {3},
pages = {e70286},
publisher = {Wiley},
issn = {2352-8737},
doi = {10.1002/trc2.70286},
url = {https://doi.org/10.1002/trc2.70286},
pmid = {42483205},
pmcid = {PMC13385209}
}

RIS

TY - JOUR
AU - Beydoun, May A.
AU - Song, Minkyo
AU - Yun, Choa
AU - Noren Hooten, Nicole
AU - Weiss, Jordan
AU - Beydoun, Hind A.
AU - Duggan, Michael R.
AU - Walker, Keenan A.
AU - Launer, Lenore J.
AU - Evans, Michele K.
AU - Zonderman, Alan B.
TI - The proteomic and metabolomic signature of inherited chromosomally integrated HHV-6 and its role in all-cause dementia and mortality risk: The UK Biobank study
T2 - Alzheimer's & dementia (New York, N. Y.)
J2 - Alzheimers Dement (N Y)
PY - 2026
DA - 2026/07/20
VL - 12
IS - 3
SP - e70286
SN - 2352-8737
PB - Wiley
DO - 10.1002/trc2.70286
UR - https://doi.org/10.1002/trc2.70286
LA - en
ER -

CSL-JSON

{
"id": "10.1002/trc2.70286",
"type": "article-journal",
"title": "The proteomic and metabolomic signature of inherited chromosomally integrated HHV-6 and its role in all-cause dementia and mortality risk: The UK Biobank study",
"container-title": "Alzheimer's & dementia (New York, N. Y.)",
"author": [
{
"family": "Beydoun",
"given": "May A."
},
{
"family": "Song",
"given": "Minkyo"
},
{
"family": "Yun",
"given": "Choa"
},
{
"family": "Noren Hooten",
"given": "Nicole"
},
{
"family": "Weiss",
"given": "Jordan"
},
{
"family": "Beydoun",
"given": "Hind A."
},
{
"family": "Duggan",
"given": "Michael R."
},
{
"family": "Walker",
"given": "Keenan A."
},
{
"family": "Launer",
"given": "Lenore J."
},
{
"family": "Evans",
"given": "Michele K."
},
{
"family": "Zonderman",
"given": "Alan B."
}
],
"container-title-short": "Alzheimers Dement (N Y)",
"volume": "12",
"issue": "3",
"page": "e70286",
"DOI": "10.1002/trc2.70286",
"PMID": "42483205",
"PMCID": "PMC13385209",
"ISSN": "2352-8737",
"publisher": "Wiley",
"URL": "https://doi.org/10.1002/trc2.70286",
"language": "en",
"issued": {
"date-parts": [
[
2026,
7,
20
]
]
}
}

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