OSCR

Biological pathways related to mirna-125a-5p in behavioral variant of frontotemporal dementia.

Code ↔ Paper

The paper beside its authors' code: matches between them have not been computed for this paper yet.

Paper

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

The paper is loaded when this pane is shown.

The authors' code

R · 102 lines · 2.5 KB · no license

  1. ##Script for the construction of the gene and pathway network based on miRNA-125a-5p.
  4. # Load libraries
  5. library(tidyverse)
  6. library(readxl)
  7. library(tidygraph)
  8. library(ggraph
  10. #Read data
  11. dados <- read_excel("data/selected_pathways_genes.xlsx")
  13. #Function to extract genes
  14. extrair_genes <- function(df, col_genes, mirna_nome) {
  15. df %>%
  16. select(`Term Name`, all_of(col_genes)) %>%
  17. rename(genes = all_of(col_genes)) %>%
  18. mutate(genes = strsplit(genes, "\n")) %>%
  19. unnest(genes) %>%
  20. mutate(
  21. genes = trimws(genes),
  22. miRNA = mirna_nome
  23. ) %>%
  24. filter(genes != "")
  25. }
  28. #Extract genes for miRNA-125a-5p
  29. df_125a <- extrair_genes(dados, "Vias 125a-5p", "hsa-miR-125a-5p")
  31. #Identify genes present in multiple pathways
  32. genes_multiplas_vias <- df_125a %>%
  33. distinct(`Term Name`, genes) %>%
  34. group_by(genes) %>%
  35. summarise(n_vias = n(), .groups = "drop") %>%
  36. filter(n_vias > 1)
  38. #Filter network
  39. rede_filtrada <- df_125a %>%
  40. filter(genes %in% genes_multiplas_vias$genes)
  42. #Create edges → vias
  43. edges_mirna_via <- rede_filtrada %>%
  44. distinct(miRNA, `Term Name`) %>%
  45. rename(from = miRNA, to = `Term Name`)
  47. #Create edges → genes
  48. edges_via_gene <- rede_filtrada %>%
  49. distinct(`Term Name`, genes) %>%
  50. rename(from = `Term Name`, to = genes)
  52. #Combine edges
  53. edges <- bind_rows(edges_mirna_via, edges_via_gene)
  55. #Create graph
  56. g <- tbl_graph(edges = edges, directed = TRUE)
  58. g <- g %>%
  59. mutate(
  60. type = case_when(
  61. name == "hsa-miR-125a-5p" ~ "miRNA",
  62. name %in% rede_filtrada$genes ~ "Gene",
  63. TRUE ~ "Pathway"
  64. ),
  65. shape = case_when(
  66. type == "miRNA" ~ "square",
  67. type == "Gene" ~ "circle",
  68. type == "Pathway" ~ "rectangle"
  69. ),
  70. color = case_when(
  71. type == "miRNA" ~ "skyblue",
  72. type == "Gene" ~ "salmon",
  73. type == "Pathway" ~ "gold"
  74. )
  75. )
  77. #Plot network
  78. set.seed(125)
  79. ggraph(g, layout = "stress") +
  80. geom_edge_link(
  81. arrow = arrow(length = unit(3, 'mm')),
  82. end_cap = circle(3, 'mm'),
  83. edge_colour = "gray50",
  84. alpha = 0.6
  85. ) +
  86. geom_node_point(aes(color = color, shape = type), size = 5) +
  87. geom_node_text(aes(label = name), repel = TRUE, size = 3, color = "black") +
  88. scale_shape_manual(name = "Tipo",
  89. values = c("Gene" = 16, "Pathway" = 22, "miRNA" = 15)) +
  90. scale_color_identity(guide = "legend", name = "Tipo") +
  91. theme_void() +
  92. theme(legend.position = "right")
  94. #Save figure
  95. ggsave(
  96. filename = "figures/network_miR125a5p.tiff",
  97. plot = p,
  98. width = 16,
  99. height = 12,
  100. dpi = 600,
  101. device = "tiff",
  102. compression = "lzw"

network_miR125a5p.R at commit 6acf7b8, no license · at the source

Overview

Authors: Jessica Diniz Pereira1, Leticia Moreira Silva1, Mhai Ozawa1, Jéssica Abdo Gonçalves Tosatti2, Stephanny Pinto Oliveira Lima2, Isabela Resende Silva2, Vinicius Ribeiro Jeunon2, Maria das Graças Carvalho1, Elisa de Paula França Resende2, Leonardo Cruz de Souza2, Paulo Caramelli2, Karina Braga Gomes1,3
ORCID iDs: Jessica Diniz Pereira, Leticia Moreira Silva, Mhai Ozawa, Jéssica Abdo Gonçalves Tosatti, Stephanny Pinto Oliveira Lima, Isabela Resende Silva, Vinicius Ribeiro Jeunon, Maria das Graças Carvalho, Elisa de Paula França Resende, Leonardo Cruz de Souza, Paulo Caramelli, Karina Braga Gomes
  1. Faculdade de Farmácia, Universidade Federal de Minas Gerais,Belo Horizonte, Minas Gerais Brazil
  2. Faculdade de Medicina, Universidade Federal de Minas Gerais,Belo Horizonte, Minas Gerais Brazil
  3. Departamento de Análises Clínicas e Toxicológicas - Faculdade de Farmácia, Universidade Federal de Minas Gerais,Avenida Presidente Antônio Carlos, 6627 - Pampulha, Belo Horizonte, CEP: 31270-901 Minas Gerais Brasil
Institutions: Universidade Federal de Minas Gerais (Brazil)
Journal: Molecular biology reports, volume 53, issue 1, article 877
Dates: received 10 February 2026; accepted 10 May 2026; published online 3 June 2026; in print 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1007/s11033-026-11965-x · PMID 42234230 · PMCID PMC13234057 · OpenAlex W7163360771
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), Alzheimer's / dementia (population), cellular / molecular (subfield)
Methods: Statistics, Machine learning, Connectivity
Keywords: Frontotemporal dementia behavioral variant, miRNAs, Biological pathways
MeSH: Frontotemporal Dementia*, MicroRNAs*, Aged, Case-Control Studies, Female, Gene Expression Regulation, Humans, Male, Middle Aged, Signal Transduction (* major topic)
Topic: Amyotrophic Lateral Sclerosis Research (Neurology, Medicine), according to OpenAlex
Funding: Universidade Federal De Minas Gerais
Citations: not cited yet (Europe PMC); 54 references in the paper

Abstract

Background: Frontotemporal dementia (FTD) comprises a group of neurodegenerative disorders that lead to progressive changes in language, behavior, personality, and movement. Accounting for approximately 60% of cases, the behavioral variant (bvFTD) represents the most common clinical presentation of FTD. MicroRNAs (miRNAs) are small non-coding RNAs involved in gene regulation and are expressed in various biological fluids. Considering bvFTD as an inflammatory disorder, this study investigated the expression of inflammation-related miRNAs in individuals with bvFTD compared with age- and sex-matched cognitively healthy controls.

Methods: Twenty patients with bvFTD and 20 cognitively healthy controls, matched for age and sex, were included in the study. Serum levels of miRNA-30c-5p and miRNA-125a-5p were analyzed.

Results: miRNA-125a-5p expression was upregulated in individuals with bvFTD compared with controls (fold change = 2.02). No significant differences between groups were observed for miRNA-30c-5p. An inverse correlation was identified between miRNA-125a-5p expression and age within the bvFTD group. Pathway enrichment analysis revealed that miRNA-125a-5p was significantly involved in the regulation of genes associated with insulin receptor signaling, SUMOylation, SUMO E3 ligase–mediated protein modification, SUMOylation of chromatin organization proteins, estrogen-dependent gene expression, extracellular exosome pathways, neuron migration, microtubule dynamics, and nervous system development.

Conclusions: These findings suggest that miRNA-125a-5p may play an important role in FTD-related biological pathways, underscoring its potential as a molecular marker in the pathophysiology of this disorder.

Supplementary Information: The online version contains supplementary material available at 10.1007/s11033-026-11965-x.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above.

jessidpereira/Script-for-the-construction-of-the-gene-and-pathway-network-based-on-miRNA-125a-5p.

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 6acf7b818a46e7218e3b3c619ce2573dd7dc75ce, 20 December 2025
Languages: R (1)
Size: 2 files, 1 script
Software Heritage: not archived
Found in: “Code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Tools: tidyverse (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
2 files
At the source: github.com/jessidpereira/Script-for-the-construction-of-the-gene-and-pathway-network-based-on-miRNA-125a-5p..git

Code availability

https://github.com/jessidpereira/Script-for-the-construction-of-the-gene-and-pathway-network-based-on-miRNA-125a-5p..git.

Reproduced under the paper's license (CC BY), from the paper cited above.

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;
  • 1 script, 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

No dataset and no data link were found in the paper.

Data availability

All data supporting the findings of this study are available within the paper and its Supplementary Information.

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 2, 28 September 2026

  • Publisher: n/a → Springer Nature

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 12 authors, 3 keywords, 10 MeSH terms, 1 funder, 53 references.

Cite

This paper

Pereira, J. D., Silva, L. M., Ozawa, M., Tosatti, J. A. G., Lima, S. P. O., Silva, I. R., Jeunon, V. R., das Graças Carvalho, M., de Paula França Resende, E., de Souza, L. C., Caramelli, P., & Gomes, K. B. (2026). Biological pathways related to mirna-125a-5p in behavioral variant of frontotemporal dementia. Molecular biology reports, 53(1), 877. https://doi.org/10.1007/s11033-026-11965-x

BibTeX

@article{pereira2026biological,
author = {Pereira, Jessica Diniz and Silva, Leticia Moreira and Ozawa, Mhai and Tosatti, Jéssica Abdo Gonçalves and Lima, Stephanny Pinto Oliveira and Silva, Isabela Resende and Jeunon, Vinicius Ribeiro and das Graças Carvalho, Maria and de Paula França Resende, Elisa and de Souza, Leonardo Cruz and Caramelli, Paulo and Gomes, Karina Braga},
title = {{Biological pathways related to mirna-125a-5p in behavioral variant of frontotemporal dementia}},
journal = {Molecular biology reports},
year = {2026},
month = jun,
volume = {53},
number = {1},
pages = {877},
publisher = {Springer Nature},
issn = {0301-4851},
doi = {10.1007/s11033-026-11965-x},
url = {https://doi.org/10.1007/s11033-026-11965-x},
pmid = {42234230},
pmcid = {PMC13234057}
}

RIS

TY - JOUR
AU - Pereira, Jessica Diniz
AU - Silva, Leticia Moreira
AU - Ozawa, Mhai
AU - Tosatti, Jéssica Abdo Gonçalves
AU - Lima, Stephanny Pinto Oliveira
AU - Silva, Isabela Resende
AU - Jeunon, Vinicius Ribeiro
AU - das Graças Carvalho, Maria
AU - de Paula França Resende, Elisa
AU - de Souza, Leonardo Cruz
AU - Caramelli, Paulo
AU - Gomes, Karina Braga
TI - Biological pathways related to mirna-125a-5p in behavioral variant of frontotemporal dementia
T2 - Molecular biology reports
J2 - Mol Biol Rep
PY - 2026
DA - 2026/06/03
VL - 53
IS - 1
SP - 877
SN - 0301-4851
PB - Springer Nature
DO - 10.1007/s11033-026-11965-x
UR - https://doi.org/10.1007/s11033-026-11965-x
LA - en
ER -

CSL-JSON

{
"id": "10.1007/s11033-026-11965-x",
"type": "article-journal",
"title": "Biological pathways related to mirna-125a-5p in behavioral variant of frontotemporal dementia",
"container-title": "Molecular biology reports",
"author": [
{
"family": "Pereira",
"given": "Jessica Diniz"
},
{
"family": "Silva",
"given": "Leticia Moreira"
},
{
"family": "Ozawa",
"given": "Mhai"
},
{
"family": "Tosatti",
"given": "Jéssica Abdo Gonçalves"
},
{
"family": "Lima",
"given": "Stephanny Pinto Oliveira"
},
{
"family": "Silva",
"given": "Isabela Resende"
},
{
"family": "Jeunon",
"given": "Vinicius Ribeiro"
},
{
"family": "das Graças Carvalho",
"given": "Maria"
},
{
"family": "de Paula França Resende",
"given": "Elisa"
},
{
"family": "de Souza",
"given": "Leonardo Cruz"
},
{
"family": "Caramelli",
"given": "Paulo"
},
{
"family": "Gomes",
"given": "Karina Braga"
}
],
"container-title-short": "Mol Biol Rep",
"volume": "53",
"issue": "1",
"page": "877",
"DOI": "10.1007/s11033-026-11965-x",
"PMID": "42234230",
"PMCID": "PMC13234057",
"ISSN": "0301-4851",
"publisher": "Springer Nature",
"URL": "https://doi.org/10.1007/s11033-026-11965-x",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
3
]
]
}
}

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

Similar papers

The papers with a page that share the most with this one: the tools found in their code, their categories, datasets, cited references and authors, the rarest counting most.

[1] doi:10.1186/s13024-026-00944-2
TDP-43: [GU]-ardian of the transcriptome.
Journal: Molecular neurodegeneration
In common: cellular / molecular, 3 references
[2] doi:10.1007/s00401-026-03042-1
Tau368 improves p-tau diagnostic accuracy for FTLD-tau from FTLD-TDP.
Journal: Acta neuropathologica
In common: Alzheimer's / dementia, 2 references
[3] doi:10.1016/j.isci.2026.115720
Progranulin deficiency in the brain activates an insulin signaling pathway that may promote neurodegeneration.
Journal: iScience
In common: cellular / molecular, 2 references
[4] doi:10.1093/braincomms/fcag341
Distinct and shared multimodal neuroimaging patterns in clinical frontotemporal dementia syndromes.
Journal: Brain communications
In common: Alzheimer's / dementia, 2 references
[5] doi:10.1093/braincomms/fcag161 [code]
Functional neuroanatomy of musical object processing in Alzheimer's disease and frontotemporal dementia.
Journal: Brain communications
In common: tidyverse, Alzheimer's / dementia, 1 reference
[6] doi:10.3389/fnagi.2026.1788991
Plasma multi-miRNA models classify Alzheimer's, Parkinson's, and Lewy body dementia.
Journal: Frontiers in aging neuroscience
In common: Alzheimer's / dementia, cellular / molecular, 1 reference
[7] doi:10.1002/glia.70163
A Cross-Disease Microglial Transcriptional Program Characterizes Neurodegeneration and Highlights SPP1 as a Biomarker.
Journal: Glia
In common: Alzheimer's / dementia, cellular / molecular, 1 reference
[8] doi:10.1111/jne.70257 [code]
A symmetric systemic challenge elicits a right-biased response mediated by vasopressin signaling.
Journal: Journal of neuroendocrinology
In common: tidyverse, cellular / molecular, 1 reference
[9] doi:10.1016/j.isci.2026.116861
NAT10 inhibition corrects nuclear defects in tau mutant human neurons and extends lifespan in a &lt;i&gt;Drosophila&lt;/i&gt; tauopathy model.
Journal: iScience
In common: Alzheimer's / dementia, cellular / molecular, 1 reference
[10] doi:10.1007/s12311-026-02006-1 [code]
Innovative 3D-Image Analysis of Cerebellar Vascularization Highlights Angiogenic Gene Dysregulations in a Murine Model of Apnea of Prematurity.
Journal: Cerebellum (London, England)
In common: tidyverse, 1 reference

Contribute

The authors of this paper can claim it, correct its record and validate its tracing map, and the maintainers of its code (its owner, or a public member of its organization) correct what it says of their repository; anyone signed in can ask for its removal. Every request goes to OSCR's own machine, which answers it; your account page follows them.

Sign in with ORCID to claim this paper as one of its authors, correct its record or validate its tracing map: when the paper's metadata lists your ORCID iD, you are recognized at once. Maintainers of its code: sign in with GitHub, then claim the repository on your account page.

Request its removal

To ask OSCR to remove this record, the copies of its authors' scripts or its tracing map, use the removal request page: signed in, you say who you are, what to remove and why, then review and confirm the request. Published rules decide every request (how).

Discussion, reproductions, activity

Discussion: questions and error reports about this paper and its code, from signed-in readers and its authors. It opens with sign-in.

Reproductions: reports from readers who ran the authors' code: what they reproduced, with which environment, commit and data. It opens with sign-in.

Activity: what happens around this paper: new versions of its record, its map's validation, discussions and reproductions. It opens with sign-in.