Identification of the Hub Genes Related to Nerve Injury-Induced Neuropathic Pain.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32508579", "kind": "science-record", "revision": 8, "content_hash": "sha256:31886af38a2bb42201a2a5ef050e9196e238e7865f57fc7b20d826ee3faf0527", "created_at": "2026-11-01T15:41:03Z", "updated_at": "2026-11-01T22:44:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the Hub Genes Related to Nerve Injury-Induced Neuropathic Pain.", "doi": "10.3389/fnins.2020.00488", "pmid": "32508579", "authors": ["Kai Wang", "Duan Yi", "Zhuoyin Yu", "Bin Zhu", "Shuiqing Li", "Xiaoguang Liu"], "journal": "Frontiers in neuroscience", "year": 2020, "abstract": "BACKGROUND: The reactivity enhancement of pain sensitive neurons in the nervous system is a feature of the pathogenesis for neuropathic pain (NP), yet the underlying mechanisms need to be fully understood. In this study, we made an attempt to clarify the NP-related hub genes and signaling pathways so as to provide effective diagnostic and therapeutic methods toward NP.\nMETHODS: Microarray expression profile GSE30691 including the mRNA-seq data of the spared nerve injury (SNI)-induced NP rats was accessed from the GEO database. Then, genes associated with NP development were screened using differential analysis along with random walk with restart (RWR). GO annotation and KEGG pathway analyses were performed to explore the biological functions and signaling pathways where the genes were activated. Afterward, protein-protein interaction (PPI) analysis and GO analysis were conducted to further identify the hub genes which showed an intimate correlation with NP development.\nRESULTS: Totally 94 genes associated with NP development were screened by differential analysis and RWR analysis, and they were observed to be predominantly enriched in hormone secretion and transport, cAMP signaling pathway and other NP occurrence associated functions and pathways. Thereafter, the 94 genes were subjected to PPI analysis to find the genes much more associated with NP and a functional module composed of 48 genes were obtained. 8 hub genes including C3, C1qb, Ccl2, Cxcl13, Timp1, Fcgr2b, Gal, and Lyz2 were eventually identified after further association and functional enrichment analyses, and the expression of these 8 genes were all higher in SNI rats by comparison with those in Sham rats.\nCONCLUSION: Based on the data collected from GEO database, this study discovered 8 hub genes that were closely related to NP occurrence and development, which help to provide potent theoretical basis for NP treatment.", "claims": [{"id": "claim-method", "statement": "Differential analysis was performed on the genes from the SNI and Sham rats in 3, 7, and 21-day three time periods using the “limma” package (Smyth, 2011), with | logFC| > 0.585 and FDR < 0.05 used as the screening threshold.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32508579", "locator": "sections[5] \"Differential Analysis\" paragraph 2", "quote": "Differential analysis was performed on the genes from the SNI and Sham rats in 3, 7, and 21-day three time periods using the “limma” package (Smyth, 2011), with | logFC| > 0.585 and FDR < 0.05 used as the screening threshold."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed in this study were downloaded and accessed from the Gene Expression Omnibus (GEO) database: https://www.ncbi.nlm.nih.gov/geo/, with accession no: GSE30691.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32508579", "locator": "sections[14] \"Data Availability Statement\" paragraph 2", "quote": "The datasets analyzed in this study were downloaded and accessed from the Gene Expression Omnibus (GEO) database: https://www.ncbi.nlm.nih.gov/geo/, with accession no: GSE30691."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32508579"], "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:GSE30691"], "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:GSE30691"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32508579", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fnins.2020.00488", "sha256": "sha256:29d6bafa56582a235b463852de73b0866cee293911587453144346e35ff7d971", "bytes": 19868, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fnins.2020.00488", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7251260", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30691", "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=GSE30691", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30691", "version": null, "note": "The datasets analyzed in this study were downloaded and accessed from the Gene Expression Omnibus (GEO) database: https://www.ncbi.nlm.nih.gov/geo/, with accession no: GSE30691.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets analyzed in this study were downloaded and accessed from the Gene Expression Omnibus (GEO) database: https://www.ncbi.nlm.nih.gov/geo/, with accession no: GSE30691.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM761214", "GSM761215", "GSM761216", "GSM761217", "GSM761218", "GSM761219", "GSM761220", "GSM761221", "GSM761222", "GSM761223", "GSM761224", "GSM761225", "GSM761226", "GSM761227", "GSM761228", "GSM761229", "GSM761230", "GSM761231", "GSM761232", "GSM761233", "GSM761234", "GSM761235", "GSM761236", "GSM761237", "GSM761238", "GSM761239", "GSM761240", "GSM761241", "GSM761242", "GSM761243", "GSM761244", "GSM761245", "GSM761246", "GSM761247", "GSM761248", "GSM761249", "GSM761250", "GSM761251", "GSM761252", "GSM761253", "GSM761254", "GSM761255", "GSM761256", "GSM761257", "GSM761258", "GSM761259", "GSM761260", "GSM761261", "GSM761262", "GSM761263", "GSM761264", "GSM761265", "GSM761266", "GSM761267", "GSM761268", "GSM761269"], "sample_count": 56, "group_sizes": null, "group_sizes_basis": null, "platform": "85", "taxon": "Rattus norvegicus", "title": "Multiple chronic pain states are associated with a common amino acid-changing allele in KCNS1", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE30691 not downloaded", "asset:data:geo:GSE30691 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differential analysis was performed on the genes from the SNI and Sham rats in 3, 7, and 21-day three time periods using the “limma” package (Smyth, 2011), with | logFC| > 0.585 and FDR < 0.05 used as the screening threshold."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE30691"], "resolved_accessions": ["GSE30691"], "statements": ["The datasets analyzed in this study were downloaded and accessed from the Gene Expression Omnibus (GEO) database: https://www.ncbi.nlm.nih.gov/geo/, with accession no: GSE30691."], "basis": "The paper names GSE30691 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:32508579", "data:geo:GSE30691"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE30691"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:14Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 15332, "completion_tokens": 1190, "cached_tokens": 785}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:32508579", "type": "paper", "label": "pmid:32508579"}, {"id": "source:pmid:32508579", "type": "manuscript", "label": "PMID 32508579 full text"}, {"id": "data:geo:GSE30691", "type": "dataset", "label": "GEO GSE30691"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32508579", "type": "paper", "label": "pmid:32508579"}, {"id": "source:pmid:32508579", "type": "manuscript", "label": "PMID 32508579 full text"}, {"id": "data:geo:GSE30691", "type": "dataset", "label": "GEO GSE30691"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32508579", "type": "extraction", "used": ["source:pmid:32508579"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE30691", "type": "accession_resolution", "used": ["data:geo:GSE30691"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:32508579", "parent_hash": "sha256:490136f3f28a8f66c6ab98d3d74c7b331bcf68a9b22e66dab6675f2bdfff6b20", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE30691 licence not read", "asset:data:geo:GSE30691 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["and therapeutic methods toward NP. METHODS: Microarray expression profile GSE30691 including the mR"], "order_basis": "paper_text_order:419", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["of the spared nerve injury (SNI)-induced NP rats was accessed from the GEO database. Then, ge", "sion of these 8 genes were all higher in SNI rats by comparison with those in Sham rats. CONCL", "in SNI rats by comparison with those in Sham rats. CONCLUSION: Based on the data collected fro"], "order_basis": "paper_text_order:530", "id": "assay:2"}, {"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": ["Differential analysis was performed on the genes from the SNI and Sham rats in 3, 7, and 21-day three time periods using the “limma” package (Smyth, 2011), with | logFC| > 0.585 and FDR < 0.05 used as the screening threshold."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}