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The cumulative impact of seizures: the science underlying how seizures beget seizures.

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The authors' code

R Markdown · 252 lines · 6.8 KB · no license

  1. ---
  2. title: "Genes4Epilepsy"
  3. subtitle: "A curated list of monogenic epilepsy genes"
  4. output:
  5. html_document:
  6. theme: cerulean
  7. self_contained: false
  8. ---
  11. ```{r setup, include=FALSE}
  12. knitr::opts_chunk$set(echo = FALSE,
  13. message = FALSE,
  14. warning = FALSE)
  15. library(tidyverse)
  16. library(DT)
  17. ```
  19. ```{r}
  20. # Assumptions
  21. # 1) List TSV files named with format EpilepsyGenes_vYYYY-MM.tsv
  22. # 2) List TSV files have columns "HGNC_ID", "Gene", "Ensemble_ID", "Entrez_ID", "OMIM_ID", "Inheritance", "Phenotype(s)"
  24. # Usage
  25. # 1) Add new version of gene list
  26. # 2) "rm -r index_files"
  27. # 3) knit index.Rmd in Rstudio and check result
  28. # 4) "git add index.Rmd index.html index_files EpilepsyGenes_v*"
  29. # 5) "git commit -m 'updated to version <VERSION>'"
  30. # 6) "git push origin main"
  31. ```
  33. ```{r functions}
  35. ensembl_url <- function(id) {
  36. str_c('<a href = "https://ensembl.org/Homo_sapiens/Gene/Summary?g=',
  37. id, '" target="_blank">', id, '</a>')
  38. }
  39. entrez_url <- function(id) {
  40. str_c('<a href = "https://www.ncbi.nlm.nih.gov/gene/?term=',
  41. id, '" target="_blank">', id, '</a>')
  42. }
  43. omim_url <- function(id) {
  44. str_c('<a href = "https://omim.org/entry/',
  45. id, '" target="_blank">', id, '</a>')
  46. }
  47. hgnc_url <- function(id) {
  48. str_c('<a href = "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/',
  49. id, '" target="_blank">', id, '</a>')
  50. }
  53. add_urls <- function(data) {
  54. mutate(
  55. data,
  56. HGNC_ID = hgnc_url(HGNC_ID),
  57. Ensemble_ID = ensembl_url(Ensemble_ID),
  58. Entrez_ID = entrez_url(Entrez_ID),
  59. OMIM_ID = omim_url(OMIM_ID)
  60. )
  61. }
  63. my_datatable <- function(data, filename) {
  64. datatable(
  65. data,
  66. rownames = FALSE,
  67. escape = FALSE,
  68. filter = 'top',
  69. extensions = 'Buttons',
  70. options = list(
  71. autoWidth=TRUE,
  72. columnDefs = list(list(width = '100px', targets = c('Gene'))),
  73. dom = 'rtipB',
  74. buttons = list(
  75. list(extend = 'csv', filename=filename),
  76. list(extend = 'excel', filename=filename, title='')
  77. ),
  78. initComplete = htmlwidgets::JS(
  79. "function(settings, json) {",
  80. "$('body').css({'font-family': 'Helvetica'});",
  81. "}"
  82. )))
  83. }
  84. ```
  87. ```{r read_lists}
  88. all_lists <-
  89. tibble(
  90. filename = list.files('.', pattern = 'EpilepsyGenes_v.*.tsv', full.names = T),
  91. version = str_extract(filename, 'v\\d{4}-\\d{2}(?=.tsv)')) %>%
  92. filter(!is.na(version)) %>%
  93. arrange(desc(version)) %>%
  94. mutate(data = map(filename,
  95. read_tsv,
  96. col_types = cols(
  97. HGNC_ID = col_character(),
  98. Gene = col_character(),
  99. Ensemble_ID = col_character(),
  100. Entrez_ID = col_integer(),
  101. OMIM_ID = col_integer(),
  102. Inheritance = col_character(),
  103. `Phenotype(s)` = col_character()),
  104. col_select = c(
  105. Gene,
  106. HGNC_ID,
  107. Ensemble_ID,
  108. Entrez_ID,
  109. OMIM_ID,
  110. Inheritance,
  111. `Phenotype(s)`),
  112. ),
  113. length = map_int(data, nrow))
  115. curr_ver <- all_lists$version[1]
  116. ```
  117. ## `r curr_ver`
  119. ```{r datatables, results='asis', eval=FALSE}
  121. all_lists %>%
  122. filter(version == curr_ver) %>%
  123. select(data) %>%
  124. unnest(data) %>%
  125. add_urls() %>%
  126. arrange(Gene) %>%
  127. my_datatable(str_c('Genes4Epilepsy_', curr_ver))
  129. ```
  132. ```{r datatables_panelapp, results='asis'}
  133. if (!require(cavalier)) {
  134. stop(str_c('Cavalier not installed - install with "devtools::install_github(\'jemunro/cavalier@dev\')"'))
  135. }
  136. # get the latest PanelApp panels
  137. panel_app <-
  138. bind_rows(
  139. cavalier::get_panelapp_panels('PAA'),
  140. cavalier::get_panelapp_panels('PAE')) %>%
  141. select(id, version) %>%
  142. filter(id %in% c('PAA:202', 'PAE:402')) %>%
  143. pmap_df(function(id, version) {
  144. cavalier::get_panelapp_panel(id, version = version)
  145. }) %>%
  146. mutate(
  147. text = if_else(list_id == 'PAA:202',
  148. 'AU:202',
  149. 'UK:402'),
  150. url = str_c(
  151. '<a href = "',
  152. if_else(list_id == 'PAA:202',
  153. 'https://panelapp-aus.org/panels/202/gene/',
  154. 'https://panelapp.genomicsengland.co.uk/panels/402/gene/'),
  155. panelapp_symbol,
  156. '" target="_blank">',
  157. text, '</a>')) %>%
  158. select(HGNC_ID = hgnc_id,
  159. PanelApp = url) %>%
  160. chop(PanelApp) %>%
  161. mutate(PanelApp = map_chr(PanelApp, str_c, collapse = ' '))
  163. all_lists %>%
  164. filter(version == curr_ver) %>%
  165. select(data) %>%
  166. unnest(data) %>%
  167. left_join(panel_app, by = 'HGNC_ID') %>%
  168. add_urls() %>%
  169. arrange(Gene) %>%
  170. my_datatable(str_c('Genes4Epilepsy_', curr_ver))
  171. ```
  174. ## Changelog
  175. ```{r changelog}
  177. all_lists %>%
  178. select(new_ver = version,
  179. new_data = data) %>%
  180. mutate(old_ver = lead(new_ver),
  181. old_data = lead(new_data)) %>%
  182. na.omit() %>%
  183. mutate(changes = map2(new_data, old_data, function(new_data, old_data) {
  185. added <-
  186. new_data %>%
  187. anti_join(old_data, by = 'HGNC_ID') %>%
  188. mutate(change = 'ADDED')
  190. removed <-
  191. old_data %>%
  192. anti_join(new_data, by = 'HGNC_ID') %>%
  193. mutate(change = 'REMOVED')
  195. updated <-
  196. new_data %>%
  197. anti_join(old_data,
  198. by = c("HGNC_ID",
  199. "Gene",
  200. "Ensemble_ID",
  201. "Entrez_ID",
  202. "OMIM_ID",
  203. "Inheritance",
  204. "Phenotype(s)")) %>%
  205. anti_join(added,
  206. by = "HGNC_ID") %>%
  207. mutate(change = 'UPDATED')
  209. bind_rows(
  210. added,
  211. updated,
  212. removed)
  214. })) %>%
  215. select(version = new_ver, changes) %>%
  216. unnest(changes) %>%
  217. select(version, change, everything()) %>%
  218. mutate(change = as.factor(change)) %>%
  219. add_urls() %>%
  220. my_datatable(str_c('Genes4Epilepsy_Changelog_v', curr_ver))
  222. ```
  224. ## All Versions TSV download
  225. ```{r past_versions}
  226. all_lists %>%
  227. select(version, download = filename, length) %>%
  228. mutate(download =
  229. basename(download) %>%
  230. (function(x)
  231. str_c('<a href="/Genes4Epilepsy/', x, '" download>', x, '</a>')
  232. )) %>%
  233. datatable(
  234. escape = FALSE,
  235. rownames = FALSE,
  236. options = list(
  237. dom = 'rtipB',
  238. initComplete = htmlwidgets::JS(
  239. "function(settings, json) {",
  240. "$('body').css({'font-family': 'Helvetica'});",
  241. "}"
  242. )))
  244. ```
  246. ## Cite
  247. If you use this Genes4Epilepsy resource, please acknowledge by citing:
  248. [Oliver KL, Scheffer IE, Bennett MF, Grinton BE, Bahlo M, Berkovic SF. Genes4Epilepsy: An epilepsy gene resource. Epilepsia. 2023 May;64(5):1368-1375. doi: 10.1111/epi.17547](https://onlinelibrary.wiley.com/doi/10.1111/epi.17547)
  250. This webpage developed by [Jacob E. Munro](https://orcid.org/0000-0002-2751-0989)

index.Rmd at commit 72364d5, no license · at the source

Overview

Authors: Richard M. Gustin1, Taha Gholipour2, Jurriaan M. Peters3
  1. Neurelis, Inc., San Diego, CA, United States
  2. Department of Neurosciences, University of California San Diego, La Jolla, CA, United States
  3. Department of Neurology, Division of Epilepsy and Neurophysiology, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
Institutions: Neurelis (United States) (United States); University of California San Diego (United States); Boston Children's Hospital (United States); Harvard University (United States)
Journal: Frontiers in neurology, volume 17, article 1793970
Dates: received 22 January 2026; accepted 6 May 2026; published online 20 May 2026
Type: Review · Language: English
License: CC BY
Identifiers: DOI 10.3389/fneur.2026.1793970 · PMID 42246053 · PMCID PMC13232767 · OpenAlex W7161842116
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: epilepsy (population), clinical / translational (subfield)
Keywords: drug-resistant epilepsy, epilepsy treatment, hyperexcitability, quality of life, seizure progression, seizure timeline
Topic: Epilepsy research and treatment (Psychiatry and Mental health, Medicine), according to OpenAlex
Citations: not cited yet (Europe PMC); 276 references in the paper

Abstract

Seizures are symptoms of epilepsy but spontaneous seizure recurrence can also be considered a biomarker of disease progression. The temporary imbalance between excitatory and inhibitory drive that culminates in a hyperexcitable, hypersynchronous state clinically observed as seizure, initiates an insidious cascade of neurochemical, structural, genetic, epigenetic, and neuroinflammatory processes that increases seizure frequency, duration, and severity. As seizure activity increases, the hyperexcitable and hypersynchronous states entrain neuronal networks, leading to a further reduction in seizure threshold and further increases in seizure frequency, duration, and severity over time. The pathological circuitry generated and sustained by epileptic events not only drive hyperexcitable states within the seizure circuit but also can affect wider network connections. These effects lead to altered network physiology, which is associated with neuropsychiatric comorbidities, such as cognitive decline and psychiatric disorders, and can impact the operation of other organ systems. Here, we review the current understanding of how seizures can hijack normal brain function and set off a cascade of pathobiological events that support continued seizure activity and epilepsy progression. Understanding the neurobiology of seizure progression is fundamental to building comprehensive treatment strategies and developing new pharmacotherapies that aim to retrain seizure circuitry, with the goal of reducing overall seizure burden, improving quality of life, and limiting disease progression.

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

Repository

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

bahlolab/genes4epilepsy

License: none: the authors keep all their rights
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: 72364d5c0ca88fe34a294d26321f80b7018fff50, 14 September 2026
Languages: JavaScript (24), R (1)
Size: 104 files, 25 scripts
Software Heritage: not archived
Found in: the text, “Genetic and epigenetic factors underlying seizur”
Holds: README, 1 notebook
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
26 files
At the source: github.com/bahlolab/genes4epilepsy

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;
  • 25 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

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

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 3 authors, 6 keywords, 276 references.

Cite

This paper

Gustin, R. M., Gholipour, T., & Peters, J. M. (2026). The cumulative impact of seizures: the science underlying how seizures beget seizures. Frontiers in neurology, 17, 1793970. https://doi.org/10.3389/fneur.2026.1793970

BibTeX

@article{gustin2026cumulative,
author = {Gustin, Richard M. and Gholipour, Taha and Peters, Jurriaan M.},
title = {{The cumulative impact of seizures: the science underlying how seizures beget seizures}},
journal = {Frontiers in neurology},
year = {2026},
month = may,
volume = {17},
pages = {1793970},
publisher = {Frontiers Media SA},
issn = {1664-2295},
doi = {10.3389/fneur.2026.1793970},
url = {https://doi.org/10.3389/fneur.2026.1793970},
pmid = {42246053},
pmcid = {PMC13232767}
}

RIS

TY - JOUR
AU - Gustin, Richard M.
AU - Gholipour, Taha
AU - Peters, Jurriaan M.
TI - The cumulative impact of seizures: the science underlying how seizures beget seizures
T2 - Frontiers in neurology
J2 - Front Neurol
PY - 2026
DA - 2026/05/20
VL - 17
SP - 1793970
SN - 1664-2295
PB - Frontiers Media SA
DO - 10.3389/fneur.2026.1793970
UR - https://doi.org/10.3389/fneur.2026.1793970
LA - en
ER -

CSL-JSON

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"id": "10.3389/fneur.2026.1793970",
"type": "article-journal",
"title": "The cumulative impact of seizures: the science underlying how seizures beget seizures",
"container-title": "Frontiers in neurology",
"author": [
{
"family": "Gustin",
"given": "Richard M."
},
{
"family": "Gholipour",
"given": "Taha"
},
{
"family": "Peters",
"given": "Jurriaan M."
}
],
"container-title-short": "Front Neurol",
"volume": "17",
"page": "1793970",
"DOI": "10.3389/fneur.2026.1793970",
"PMID": "42246053",
"PMCID": "PMC13232767",
"ISSN": "1664-2295",
"publisher": "Frontiers Media SA",
"URL": "https://doi.org/10.3389/fneur.2026.1793970",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
20
]
]
}
}

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