A Bioinformatics Study of Differentially Expressed Genes in Microarrays of Dorsal Root Ganglia from Rat Models of Neuropathic Pain.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35165251", "kind": "science-record", "revision": 5, "content_hash": "sha256:f53109ab55a000dbf83368c48bd428a0609484191de6e331ad2581157be0ca68", "created_at": "2026-11-01T17:36:55Z", "updated_at": "2026-11-01T22:05:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A Bioinformatics Study of Differentially Expressed Genes in Microarrays of Dorsal Root Ganglia from Rat Models of Neuropathic Pain.", "doi": "10.12659/MSM.934122", "pmid": "35165251", "authors": ["Yongle Wu", "Hai Nie"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2022, "abstract": "BACKGROUND Neuropathic pain is a significant complication of nerve injury. This study aimed to conduct bioinformatics analysis of differentially expressed genes (DEGs) in microarrays of dorsal root ganglia (DRG) from rat models of neuropathic pain, based on 4 GEO datasets: GSE15041, GSE38038, GSE2884, and GSE24982. MATERIAL AND METHODS We retrieved the 4 microarray datasets, which were generated using DRG samples collected in the early and late stages after spinal nerve ligation in rats. The common DEGs (co-DEGs) were identified and then subjected to Gene Ontology, pathway enrichment, and Protein-protein interaction network analyses. Drugs targeting the identified hub genes were analyzed using the Drug Gene Interaction Database. RESULTS We identified 75 early-stage co-DEGs, which were enriched in chromosome segregation and protein catabolic processes, cytosol and extracellular exosome components, and ATP binding function and metabolic pathways. We identified 29 late-stage co-DEGs, which were enriched in protein tetramerization and drug responses, extracellular and membrane raft components, and protein homodimerization and binding functions and calcium signaling pathways. We also identified several hub genes, including Snap25 (synaptosome-associated protein of 25 kDa), Vamp2 (vesicle associated membrane protein 2), and Sf3b1 (splicing factor 3b subunit 1), the first 2 of which can be targeted by botulinum toxin derivatives. SNAP25 plays a role in synaptogenesis and the exocytotic release of neurotransmitters, and VAMP2 participates in neurotransmitter release at a step between docking and fusion. CONCLUSIONS The present study reveals new mechanisms of neuropathic pain and provides key genes, including SNAP25 and VAMP2, for future studies.", "claims": [{"id": "claim-method", "statement": "DEGs between SNL and sham DRG specimens were identified via GEO2R online tools (https://www.ncbi.nlm.nih.gov/geo/geo2r/) with log fold change greater than 1.2 or log fold change less than −1.2 and an adjusted P value less than 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35165251", "locator": "sections[4] \"Data Processing\" paragraph 2", "quote": "DEGs between SNL and sham DRG specimens were identified via GEO2R online tools (https://www.ncbi.nlm.nih.gov/geo/geo2r/) with log fold change greater than 1.2 or log fold change less than −1.2 and an adjusted P value less than 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray datasets GSE15041, GSE38038, GSE2884, and GSE24982 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) [6–8]. The investigators collected the DRG samples on day 7 for GSE15041 and GSE38038 and on day 28 for GSE2884 and GSE24982 datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35165251", "locator": "sections[3] \"Data Collection\" paragraph 2", "quote": "The microarray datasets GSE15041, GSE38038, GSE2884, and GSE24982 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) [6–8]. The investigators collected the DRG samples on day 7 for GSE15041 and GSE38038 and on day 28 for GSE2884 and GSE24982 datasets."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 75 early-stage co-DEGs at day 7 and 29 late-stage co-DEGs at day 28, with no common DEGs between the two stages.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35165251", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified 75 early-stage co-DEGs, which were enriched in chromosome segregation and protein catabolic processes, cytosol and extracellular exosome components, and ATP binding function and metabolic pathways."}, {"asset": "source:pmid:35165251", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified 29 late-stage co-DEGs, which were enriched in protein tetramerization and drug responses, extracellular and membrane raft components, and protein homodimerization and binding functions and calcium signaling pathways."}, {"asset": "source:pmid:35165251", "locator": "sections[9] \"Identification of DEGs\" paragraph 2", "quote": "There was no co-DEG between the DRG collected on day 7 and day 28, suggesting that the molecular mechanisms of neuropathic pain are different between the early and late stages."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 75 early-stage co-DEGs at day 7 and 29 late-stage co-DEGs at day 28, with no common DEGs between the two stages.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:35165251"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE15041"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE15041"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35165251", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.934122", "sha256": "sha256:22bdf5afa4dcae84e49e8b805a228610aefc031e591a17f74cafe894db388aa5", "bytes": 26039, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.934122", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8857866", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15041", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE15041", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15041", "version": null, "note": "The microarray datasets GSE15041, GSE38038, GSE2884, and GSE24982 were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) [6–8]. 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