Identification of the common differentially expressed genes and pathogenesis between neuropathic pain and aging.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36340779", "kind": "science-record", "revision": 5, "content_hash": "sha256:c974abacd61d6b6976e1d347fa9c8753c42cf292ef895e578b1160081b27d75c", "created_at": "2026-11-01T18:15:46Z", "updated_at": "2026-11-01T22:50:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the common differentially expressed genes and pathogenesis between neuropathic pain and aging.", "doi": "10.3389/fnins.2022.994575", "pmid": "36340779", "authors": ["Qingqing Ye", "Zhensheng Huang", "Weicheng Lu", "Fang Yan", "Weian Zeng", "Jingdun Xie", "Weiqiang Zhong"], "journal": "Frontiers in neuroscience", "year": 2022, "abstract": "Background: Neuropathic pain is a debilitating disease caused by damage or diseases of the somatosensory nervous system. Previous research has indicated potential associations between neuropathic pain and aging. However, the mechanisms by which they are interconnected remain unclear. In this study, we aim to identify the common differentially expressed genes (co-DEGs) between neuropathic pain and aging through integrated bioinformatics methods and further explore the underlying molecular mechanisms.\nMethods: The microarray datasets GSE24982, GSE63442, and GSE63651 were downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and co-DEGs were first identified. Functional enrichment analyses, protein-protein Interaction (PPI) network, module construction and hub genes identification were performed. Immune infiltration analysis was conducted. Targeted transcription factors (TFs), microRNAs (miRNAs) and potential effective drug compounds for hub genes were also predicted.\nResults: A total of 563 and 1,250 DEGs of neuropathic pain and aging were screened, respectively. 16 genes were further identified as co-DEGs. The functional analysis emphasizes the vital roles of the humoral immune response and complement and coagulation cascades in these two diseases. Cxcl14, Fblim1, RT1-Da, Serping1, Cfd, and Fcgr2b were identified as hub genes. Activated B cell, mast cell, activated dendritic cell, CD56 bright natural killer cell, effector memory CD8 + T cell, and type 2 T helper cell were significantly up-regulated in the pain and aging condition. Importantly, hub genes were found to correlate with the activated B cell, activated dendritic cell, Gamma delta T cell, central memory CD4 + T cell and mast cell in pain and aging diseases. Finally, Spic, miR-883-5p, and miR-363-5p et al. were predicted as the potential vital regulators for hub genes. Aldesleukin, Valziflocept, MGD-010, Cinryze, and Rhucin were the potential effective drugs in neuropathic pain and aging.\nConclusion: This study identified co-DEGs, revealed molecular mechanisms, demonstrated the immune microenvironment, and predicted the possible TFs, miRNAs regulation networks and new drug targets for neuropathic pain and aging, providing novel insights into further research.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were identified based on R packages “limma” and “impute” (Ritchie et al., 2015; Hastie et al., 2021). DEGs were defined as genes with adjusted P-value < 0.05 and | logFC (fold change) | ≥ 0.58 in the pain datasets, and genes with p-value < 0.05 and | logFC (fold change) | ≥ 0.58 in the aging dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36340779", "locator": "sections[4] \"Identification of differentially expressed genes and common differentially expressed genes\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were identified based on R packages “limma” and “impute” (Ritchie et al., 2015; Hastie et al., 2021). DEGs were defined as genes with adjusted P-value < 0.05 and | logFC (fold change) | ≥ 0.58 in the pain datasets, and genes with p-value < 0.05 and | logFC (fold change) | ≥ 0.58 in the aging dataset."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36340779", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 563 and 1,250 DEGs of neuropathic pain and aging were screened, respectively. 16 genes were further identified as co-DEGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36340779", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 563 and 1,250 DEGs of neuropathic pain and aging were screened, respectively. 16 genes were further identified as co-DEGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 563 and 1,250 DEGs of neuropathic pain and aging were screened, respectively. 16 genes were further identified as co-DEGs.", "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:36340779"], "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:GSE24982"], "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:GSE24982"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36340779", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnins.2022.994575", "sha256": "sha256:6a2ec5102b062c47802b76d4d346e2b52e29a470e8481d6a0a53fee5319049c0", "bytes": 54141, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fnins.2022.994575", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9626798", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE24982", "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=GSE24982", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE24982", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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Methods: The microarray datasets GSE24982, GSE63442, and GSE63651 we"], "order_basis": "paper_text_order:586", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) were identified based on R packages “limma” and “impute” (Ritchie et al., 2015; Hastie et al., 2021). DEGs were defined as genes with adjusted P-value < 0.05 and | logFC (fold change) | ≥ 0.58 in the pain datasets, and genes with p-value < 0.05 and | logFC (fold change) | ≥ 0.58 in the aging dataset."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}