{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31696225", "kind": "science-record", "revision": 8, "content_hash": "sha256:79405d89595426773d448a211b831a23e64336bfee027999c041e6e172e2ef1a", "created_at": "2026-11-01T15:40:51Z", "updated_at": "2026-11-01T22:00:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Weighted gene co-expression network analysis reveals specific modules and hub genes related to neuropathic pain in dorsal root ganglions.", "doi": "10.1042/BSR20191511", "pmid": "31696225", "authors": ["Nan Cheng", "Zheng Zhang", "Yue Guo", "Zhuo-Lin Qiu", "Jing-Yi Du", "Zi-Qing Hei", "Xiang Li"], "journal": "Bioscience reports", "year": 2019, "abstract": "Neuropathic pain is a common, debilitating clinical issue. Here, the weighted gene co-expression network analysis (WGCNA) was used to identify the specific modules and hub genes that are related to neuropathic pain. The microarray dataset of a neuropathic rat model induced by tibial nerve transection (TNT), including dorsal root ganglion (DRG) tissues from TNT model (n=7) and sham (n=8) rats, was downloaded from the ArrayExpress database (E-MTAB-2260). The co-expression network modules were identified by the WGCNA package. The protein-protein interaction (PPI) network was constructed, and the node with highest level of connectivity in the network were identified as the hub gene. A total of 1739 genes and seven modules were identified. The most significant module was the brown module, which contained 215 genes that were primarily associated with the biological process (BP) of the defense response and molecular function of calcium ion binding. Furthermore, C-C motif chemokine ligand 2 (Ccl2), Fos and tissue inhibitor of metalloproteinase 1 (Timp1) which were identified as the hub genes in the PPI network and two subnetworks separately. The in vivo studies validated that mRNA and protein levels of Ccl2, Fos and Timp1 were up-regulated in DRG and spinal cord tissues after TNT. The present study offers novel insights into the molecular mechanisms of neuropathic pain in the context of peripheral nerve injury.", "claims": [{"id": "claim-method", "statement": "We performed R package ‘WGCNA’ to construct weighted co-expression networks that could depict the correlation of gene expression patterns and highlight the highly correlated gene modules [3]. The microarray dataset of neuropathic pain (E-MTAB-2260), published by Jamieson and colleagues [7], was downloaded from the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/), which includes 15 DRG tissues from tibial nerve transection (TNT) model (n=7) and sham (n=8) rats.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31696225", "locator": "sections[4] \"WGCNA\" paragraph 2", "quote": "We performed R package ‘WGCNA’ to construct weighted co-expression networks that could depict the correlation of gene expression patterns and highlight the highly correlated gene modules [3]."}, {"asset": "source:pmid:31696225", "locator": "sections[3] \"Microarray data sources and processing\" paragraph 2", "quote": "The microarray dataset of neuropathic pain (E-MTAB-2260), published by Jamieson and colleagues [7], was downloaded from the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/), which includes 15 DRG tissues from tibial nerve transection (TNT) model (n=7) and sham (n=8) rats."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray dataset of neuropathic pain (E-MTAB-2260), published by Jamieson and colleagues [7], was downloaded from the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/), which includes 15 DRG tissues from tibial nerve transection (TNT) model (n=7) and sham (n=8) rats.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31696225", "locator": "sections[3] \"Microarray data sources and processing\" paragraph 2", "quote": "The microarray dataset of neuropathic pain (E-MTAB-2260), published by Jamieson and colleagues [7], was downloaded from the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/), which includes 15 DRG tissues from tibial nerve transection (TNT) model (n=7) and sham (n=8) rats."}], "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:31696225"], "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. 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"Term (BP)", "P-value", "Term (MF)", "P-value", "Term (CC)", "P-value", "Term", "P-value"], ["Brown (gene count: 215)", "Inflammatory response", "2.957e-11", "Metal ion transmembrane transport activity", "4.229e-7", "Neuron to neuron synapse", "2.144e-14", "Complement and coagulation cascades", "8.124e-7"], ["", "Defense response", "5.044e-11", "Channel activity", "5.719e-7", "Extracellular matrix", "4.743e-14", "Glutamatergic synapse", "3.179e-6"], ["", "Regulation of ion transmembrane transport", "7.044e-11", "Passive transmembrane transporter activity", "6.397e-7", "Synaptic membrane", "4.743e-14", "Circadian entrainment", "2.777e-5"], ["Green (gene count: 72)", "No genes were enriched", "No P-value", "No genes were enriched", "No P-value", "No genes were enriched", "No P-value", "No genes were enriched", "No P-value"], ["Gray (gene count: 72)", "No genes were enriched", "No P-value", "Receptor signaling complex scaffold activity", "4.231e-3", "Postsynaptic membrane", "1.071e-3", "No genes were enriched", "No P-value"], ["", "", "", "Transmembrane receptor protein kinase activity", "2.532e-3", "Synaptic membrane", "1.162e-3", "", ""], ["", "", "", "", "", "Extracellular matrix", "1.202e-3", "", ""], ["Blue (gene count: 500)", "Regulation of transporter activity", "1.077e-14", "Drug transmembrane transporter activity", "2.658e-5", "Neuron to neuron synapse", "1.886e-6", "Glutamatergic synapse", "2.971e-6"], ["", "Amino acid transport", "1.421e-14", "Postsynaptic neurotransmitter receptor activity", "2.759e-5", "Synaptic membrane", "1.886e-6", "Neuroactive ligand–receptor interaction", "4.872e-5"], ["", "Neurotransmitter transport", "2.254e-14", "Structural constituent of postsynaptic specialization", "5.778e-5", "Postsynaptic specialization", "2.965e-6", "Circadian entrainment", "4.871e-5"], ["Yellow (gene count: 151)", "Extracellular structure organization", "5.787e-14", "Extracellular matrix structural constituent", "6.985e-9", "Collagen-containing extracellular matrix", "2.198e-18", "ECM–receptor interaction", "1.127e-7"], ["", "Extracellular matrix organization", "1.778e-13", "Platelet-derived growth factor binding", "2.143e-6", "Extracellular matrix", "8.979e-18", "Protein digestion and absorption", "1.181e-7"], ["", "Collagen fibril organization", "2.054e-7", "Sphingolipid binding", "1.211e-4", "Collagen trimer", "5.774e-12", "Focal adhesion", "8.861e-6"], ["Red (gene count: 60)", "No genes were enriched", "No P-value", "No genes were enriched", "No P-value", "cis-Golgi network", "4.742e-2", "No genes were enriched", "No P-value"], ["", "", "", "", "", "Nuclear chromatin", "4.742e-2", "", ""], ["Turquoise (gene count: 669)", "Negative regulation of neuron differentiation", "8.699e-8", "Metal ion transmembrane transporter activity", "1.974e-7", "Neuron to neuron synapse", "3.608e-13", "Long-term depression", "2.665e-4"], ["", "Multicellular organismal response to stress", "2.247e-7", "Cation channel activity", "6.125e-7", "Asymmetric synapse", "1.604e-10", "Proximal tubule bicarbonate reclamation", "2.665e-4"], ["", "Negative regulation of nervous system development", "4.403e-7", "Substrate-specific channel activity", "6.806e-6", "Postsynaptic density", "2.025e-10", "Glutamatergic synapse", "2.665e-4"]], "row_count": 20, "column_count": 9, "numeric_cells": 62, "header_rows": 2, "locator": "section[16]/table-wrap[1]#T3"}}], "gaps": ["asset:data:geo:E-MTAB-2260 not downloaded", "asset:data:geo:E-MTAB-2260 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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"}}, {"id": "method-2", "family": null, "specific": null, "label": "Weighted 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The microarray dataset of neuropathic pain (E-MTAB-2260), published by Jamieson and colleagues [7], was downloaded from the ArrayExpress database (http://www.ebi.ac.uk/arrayexpress/), which includes 15 DRG tissues from tibial nerve transection (TNT) model (n=7) and sham (n=8) rats."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}