Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice.

Code ↔ Paper

7 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.

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[1] § Results › Spatial patterns of gene expression in the forebrain ↔ preprocessing/functions/umap_feature_expression_plot.R, lines 195–263 · score 0.68 · Adora2a, Ppp1r2, Drd1, Drd2, Ecel1, Gad2
[2] § Results › Spatial patterns of gene expression in the forebrain ↔ preprocessing/risperidone/ris-umap-genes.R, the whole file · a weak match · score 0.67 · Adora2a, Ppp1r2, Drd1, Drd2, Ecel1, Gad2
[3] § Methods › Cluster identification and marker validation ↔ preprocessing/functions/functions-spatial-data.R, lines 71–132 · score 0.66 · Principal component, Seurat, UMAP, neighbor, variable
[4] § Methods › Cluster identification and marker validation ↔ preprocessing/old-scripts/deseq-test-analysis.R, lines 392–476 · score 0.64 · variance stabilizing transformation, log2 fold change, Clusters
[5] § Methods › Differential gene expression analysis ↔ preprocessing/functions/statistics-functions-v2.R, lines 186–234 · score 0.57 · log2 fold change, quantile normalization, assignments, clustering resolution, transcript
[6] § Methods › Peak processing, validation, and custom reference generation ↔ preprocessing/old-scripts/reduction-peaks.R, lines 333–414 · score 0.52 · amplitude, log10, coverage, BAM, summit, ratio
[7] § Results › Enrichment analysis ↔ preprocessing/clozapine/supplementaryAnalysis_paper_03.12.2025.R, the whole file · a weak match · score 0.50 · Cacna1i, Bhlhe40, Phactr3, Homer1, Kalrn, Olig2

Paper

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The authors' code

R · 267 lines · 10 KB · no license · 1 match

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Overview

Authors: Magdalena Ziemiańska¹, Mateusz Zięba², Anna Radlicka-Borysewska¹, Łukasz Szumiec¹, Sławomir Gołda¹, Małgorzata Borczyk², Marcin Piechota², Michał Korostyński², Jan Rodriguez Parkitna¹

Institutions: Maj Institute of Pharmacology (Poland); Polish Academy of Sciences (Poland)

Journal: Frontiers in molecular neuroscience, volume 19, article 1844705

Dates: received 1 April 2026; accepted 12 May 2026; published online 29 May 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.3389/fnmol.2026.1844705 · PMID 42293048 · PMCID PMC13260059 · OpenAlex W7162765275

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: genetics / omics (modality), mouse (organism), schizophrenia / psychosis (population), cellular / molecular (subfield)

Methods: Statistics, Smoothing, state filtering, decompositions, Preprocessing

Keywords: antipsychotics, forebrain, gene expression, mouse, risperidone, schizophrenia, spatial transcriptomics

Topic: Neurogenesis and neuroplasticity mechanisms (Developmental Neuroscience, Neuroscience), according to OpenAlex

Citations: not cited yet (Europe PMC); 79 references in the paper

Research resources: RRID:SCR_001575, RRID:SCR_002105, RRID:SCR_014583, 000 Sequencing System RRID:SCR_016387, RRID:SCR_018555, 100 RRID:SCR_019715, RRID:SCR_020214, RRID:SCR_023571, RRID:SCR_025848

Abstract

Introduction: Risperidone is a widely used antipsychotic that reduces psychotic symptoms through modulation of monoaminergic signaling. At the cellular level, however, its effects extend beyond receptor antagonism and induce spatially discrete transcriptional responses across forebrain structures, particularly in the basal ganglia and frontal cortex.

Methods: We applied sequencing-based spatial transcriptomics to the forebrain of male C57BL/6N mice following acute risperidone treatment (0.5 mg/kg, i.p.). Unsupervised clustering of spatial transcriptomic profiles accurately delineated cortical divisions, cortical layers, and basal ganglia subregions. Differential expression analysis within anatomically defined clusters, performed using a customized statistical framework, revealed transcriptional patterns that were highly structure-specific and distinct between cortical and basal ganglia regions.

Results: Acute risperidone treatment significantly affected 95 transcripts across 12 brain regions. The most prominent transcriptional changes were concentrated in ventral forebrain structures, including the olfactory tubercle (25 differentially expressed transcripts), diagonal band nucleus (22), corpus callosum and commissures (13), and lateral septal nucleus (9). Importantly, 18 of these 95 genes have previously been implicated in schizophrenia, including Olig2, Smpd3, and Cacna1i.

Discussion: Together, these findings indicate that acute treatment with risperidone in male mice exerts pronounced molecular effects in medial and ventral forebrain regions with high oligodendrocyte and glial cell abundance. Moreover, enrichment analysis points to a molecular convergence between risperidone-induced transcription and genetic pathways implicated in schizophrenia.

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

Repositories

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macs3-project/MACS

License: BSD-3-Clause

State: the link answers, verified on 28 September 2026

Evidence: files inventoried

Commit: c5443190e3edfeb301cc94acf450e2b2c026a223, 25 September 2026

Languages: Python (75), C/C++ (17), C (16), Jupyter (4), Shell (2)

Size: 365 files, 114 scripts

Software Heritage: archived

Found in: the end of the paper

Holds: README, license file, environment (pyproject.toml, requirements.txt, setup.py), tests, continuous integration, documentation, 4 notebooks

Not found: CITATION.cff

Tools: NumPy (26 files), pandas (6 files), anndata (4 files), SciPy (4 files), Matplotlib (3 files), PyTorch (1 file), Scanpy (1 file)

Availability: 1 check, the latest on 28 September 2026: the link answers

28 September 2026: the link answers

116 files

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MACS3/Commands/bdgcmp_cmd.py — Python, 92 lines
MACS3/Commands/bdgdiff_cmd.py — Python, 107 lines
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MACS3/Commands/bdgpeakcall_cmd.py — Python, 65 lines
MACS3/Commands/callpeak_cmd.py — Python, 417 lines
MACS3/Commands/callvar_cmd.py — Python, 351 lines
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MACS3/Commands/hmmratac_cmd.py — Python, 652 lines
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MACS3/Commands/refinepeak_cmd.py — Python, 120 lines
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MACS3/IO/OutputWriter.py — Python, 301 lines
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MACS3/IO/PeakIO.py — Python, 1,577 lines
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MACS3/Signal/CallPeakUnit.py — Python, 2,294 lines
MACS3/Signal/FixWidthTrack.py — Python, 884 lines
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MACS3/Signal/HMMR_HMM.py — Python, 134 lines
MACS3/Signal/HMMR_Signal_Processing.py — Python, 276 lines
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MACS3/Signal/__init__.py — Python, 1 line
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MACS3/Signal/cPosValCalculation.h — C/C++, 41 lines
MACS3/Signal/swalign.c — C, 358 lines
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MACS3/Utilities/Constants.py — Python, 14 lines
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MACS3/Utilities/__init__.py — Python, 1 line
MACS3/__init__.py — Python, 1 line
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MACS3/fermi-lite/bubble.c — C, 366 lines
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MACS3/fermi-lite/kthread.c — C, 67 lines
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MACS3/fermi-lite/misc.c — C, 294 lines
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MACS3/fermi-lite/rope.c — C, 219 lines
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scripts/summarize_macs_version_survey.py — Python, 108 lines
setup.py — Python, 201 lines
test/jaccard.py — Python, 50 lines
test/test_BAMBAI.py — Python, 110 lines
test/test_BedGraph.py — Python, 100 lines
test/test_BedGraphIO.py — Python, 113 lines
test/test_CallPeakUnit.py — Python, 203 lines
test/test_FixWidthTrack.py — Python, 92 lines
test/test_HMMR_HMM.py — Python, 96 lines
test/test_HMMR_poisson.py — Python, 89 lines
test/test_PairedEndTrack.py — Python, 440 lines
test/test_Parser.py — Python, 48 lines
test/test_PeakDetect.py — Python, 218 lines
test/test_PeakIO.py — Python, 54 lines
test/test_PeakModel.py — Python, 145 lines
test/test_Pileup.py — Python, 452 lines
test/test_Prob.py — Python, 176 lines
test/test_Region.py — Python, 103 lines
test/test_ScoreTrack.py — Python, 300 lines
test/test_SignalProcessing.py — Python, 136 lines
test/test_online.py — Python, 42 lines
LICENSE — License, 28 lines
README.md — Text, 94 lines

At the source: github.com/macs3-project/MACS

ippas/ifpan-janrod-spatial

License: none: the authors keep all their rights

State: the link answers, verified on 28 September 2026

Evidence: files inventoried

Commit: 03f0a59895f28cd124562d4e07b397f41684a177, 1 September 2026

Languages: R (204), Python (23), Shell (8)

Size: 286 files, 235 scripts

Software Heritage: not archived

Found in: the end of the paper

Holds: README, environment (.devcontainer/devcontainer.json, preprocessing/dockerfiles/Dockerfile.peaks, preprocessing/dockerfiles/Dockerfile.r4.0.3-seurat4-package-version-spatial, preprocessing/dockerfiles/Dockerfile.r4.0.3-seurat4-package-version-spatial-update, preprocessing/dockerfiles/Dockerfile.r4.0.3-seurat4-shiny, preprocessing/dockerfiles/Dockerfile.r4.0.3-seurat4-spatial, preprocessing/dockerfiles/Dockerfile.r4.3.0-seurat5, preprocessing/dockerfiles/Dockerfile.rstudio, preprocessing/dockerfiles/Dockerfile.shiny)

Not found: license file, CITATION.cff, tests, continuous integration, documentation

Tools: tidyverse (81 files), circlize (28 files), ComplexHeatmap (28 files), pandas (21 files), patchwork (17 files), scikit-learn (15 files), Matplotlib (12 files), NumPy (12 files), edgeR (11 files), ggplot2 (11 files), anndata (6 files), Seurat (4 files), BEDTools (3 files), SciPy (3 files), igraph (2 files), limma (2 files), pysam (2 files), SAMtools (2 files), seaborn (2 files), cowplot (1 file), data.table (1 file), DESeq2 (1 file), psych (1 file), reshape2 (1 file), Scanpy (1 file)

Availability: 1 check, the latest on 28 September 2026: the link answers

28 September 2026: the link answers

236 files, not copied: shown from their source

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preprocessing/bed2gtf-spaceranger.py — Python, 91 lines, shown from its source
preprocessing/clozapine/clozapine-analysis-half.R — R, 140 lines, shown from its source
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README.md — Text, 91 lines, shown from its source

At the source: github.com/ippas/ifpan-janrod-spatial

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:

2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
349 scripts, each with its path and the digest of its content;
7 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

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

Data availability statement

The RNAseq dataset generated for this study can be found in the Sequence Read Archive, https://www.ncbi.nlm.nih.gov/, under accession number PRJNA1143882.

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, 28 September 2026: the first record

Recorded: type, language, journal, volume, pages, dates, 9 authors, 7 keywords, 79 references, 9 RRIDs.

Cite

This paper

Ziemiańska, M., Zięba, M., Radlicka-Borysewska, A., Szumiec, Ł., Gołda, S., Borczyk, M., Piechota, M., Korostyński, M., & Rodriguez Parkitna, J. (2026). Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice. Frontiers in molecular neuroscience, 19, 1844705. https://doi.org/10.3389/fnmol.2026.1844705

BibTeX

@article{ziemianska2026risperidone, author = {Ziemiańska, Magdalena and Zięba, Mateusz and Radlicka-Borysewska, Anna and Szumiec, Łukasz and Gołda, Sławomir and Borczyk, Małgorzata and Piechota, Marcin and Korostyński, Michał and Rodriguez Parkitna, Jan}, title = {{Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice}}, journal = {Frontiers in molecular neuroscience}, year = {2026}, month = may, volume = {19}, pages = {1844705}, publisher = {Frontiers Media SA}, issn = {1662-5099}, doi = {10.3389/fnmol.2026.1844705}, url = {https://doi.org/10.3389/fnmol.2026.1844705}, pmid = {42293048}, pmcid = {PMC13260059} }

RIS

TY - JOUR AU - Ziemiańska, Magdalena AU - Zięba, Mateusz AU - Radlicka-Borysewska, Anna AU - Szumiec, Łukasz AU - Gołda, Sławomir AU - Borczyk, Małgorzata AU - Piechota, Marcin AU - Korostyński, Michał AU - Rodriguez Parkitna, Jan TI - Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice T2 - Frontiers in molecular neuroscience J2 - Front Mol Neurosci PY - 2026 DA - 2026/05/29 VL - 19 SP - 1844705 SN - 1662-5099 PB - Frontiers Media SA DO - 10.3389/fnmol.2026.1844705 UR - https://doi.org/10.3389/fnmol.2026.1844705 LA - en ER -

CSL-JSON

{ "id": "10.3389/fnmol.2026.1844705", "type": "article-journal", "title": "Risperidone regulates the expression of schizophrenia-related genes in the forebrain of adult male mice", "container-title": "Frontiers in molecular neuroscience", "author": [ { "family": "Ziemiańska", "given": "Magdalena" }, { "family": "Zięba", "given": "Mateusz" }, { "family": "Radlicka-Borysewska", "given": "Anna" }, { "family": "Szumiec", "given": "Łukasz" }, { "family": "Gołda", "given": "Sławomir" }, { "family": "Borczyk", "given": "Małgorzata" }, { "family": "Piechota", "given": "Marcin" }, { "family": "Korostyński", "given": "Michał" }, { "family": "Rodriguez Parkitna", "given": "Jan" } ], "container-title-short": "Front Mol Neurosci", "volume": "19", "page": "1844705", "DOI": "10.3389/fnmol.2026.1844705", "PMID": "42293048", "PMCID": "PMC13260059", "ISSN": "1662-5099", "publisher": "Frontiers Media SA", "URL": "https://doi.org/10.3389/fnmol.2026.1844705", "language": "en", "issued": { "date-parts": [ [ 2026, 5, 29 ] ] } }

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