Identification of Immune-Related Biomarkers for Sciatica in Peripheral Blood.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34925462", "kind": "science-record", "revision": 5, "content_hash": "sha256:26f4da97d649770c8645e3e368d5e9a9d06ca56a38065e6d1494d88da1569eb6", "created_at": "2026-11-01T17:36:38Z", "updated_at": "2026-11-01T22:48:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Immune-Related Biomarkers for Sciatica in Peripheral Blood.", "doi": "10.3389/fgene.2021.781945", "pmid": "34925462", "authors": ["Xin Jin", "Jun Wang", "Lina Ge", "Qing Hu"], "journal": "Frontiers in genetics", "year": 2021, "abstract": "Objective: Sciatica pertains to neuropathic pain that has been associated with inflammatory response. We aimed to identify significant immune-related biomarkers for sciatica in peripheral blood. Methods: We utilized the GSE150408 expression profiling data from the Gene Expression Omnibus (GEO) database as the training dataset and extracted immune-related genes for further analysis. Differentially expressed immune-related genes (DEIRGs) between healthy controls and patients with sciatica were selected using the \"limma\" package and verified in clinical specimens by quantitative reverse transcription PCR (RT-qPCR). A diagnostic immune-related gene signature was established using the training model and random forest (RF), generalized linear model (GLM), and support vector machine (SVM) models. Sciatica patient subtypes were identified using the consensus clustering method. Results: Thirteen significant DEIRGs were acquired, of which five (CRP, EREG, FAM19A4, RLN1, and WFIKKN1) were selected to establish a diagnostic immune-related gene signature according to the most appropriate training model, namely, the RF model. A clinical application nomogram model was established based on the expression level of the five DEIRGs. The sciatica patients were divided into two subtypes (C1 and C2) according to the consensus clustering method. Conclusions: Our research established a diagnostic five immune-related gene signature to discriminate sciatica and identified two sciatica subtypes, which may be beneficial to the clinical diagnosis and treatment of sciatica.", "claims": [{"id": "claim-method", "statement": "The “limma” package was used to screen DEIRGs between 17 healthy controls and 42 sciatica patients with the inclusion criteria log∣FC∣ > 0.2 and p < 0.001.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34925462", "locator": "sections[5] \"Identification of DEIRGs\" paragraph 2", "quote": "The “limma” package was used to screen DEIRGs between 17 healthy controls and 42 sciatica patients with the inclusion criteria log∣FC∣ > 0.2 and p < 0.001."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34925462", "locator": "sections[19] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Thirteen significant DEIRGs were acquired, of which five (CRP, EREG, FAM19A4, RLN1, and WFIKKN1) were selected to establish a diagnostic immune-related gene signature according to the most appropriate training model, namely, the RF model.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34925462", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Thirteen significant DEIRGs were acquired, of which five (CRP, EREG, FAM19A4, RLN1, and WFIKKN1) were selected to establish a diagnostic immune-related gene signature according to the most appropriate training model, namely, the RF model."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Thirteen significant DEIRGs were acquired, of which five (CRP, EREG, FAM19A4, RLN1, and WFIKKN1) were selected to establish a diagnostic immune-related gene signature according to the most appropriate training model, namely, the RF model.", "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:34925462"], "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:GSE150408"], "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:GSE150408"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34925462", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2021.781945", "sha256": "sha256:1bd6ff3ca0817a0407bdb4b65c41bcaa9efc84c9e73a0f10ad376c45450ebd4b", "bytes": 29356, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2021.781945", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8677837", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE150408", "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=GSE150408", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE150408", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4548691", "GSM4548692", "GSM4548693", "GSM4548694", "GSM4548695", "GSM4548696", "GSM4548697", "GSM4548698", "GSM4548699", "GSM4548700", "GSM4548701", "GSM4548702", "GSM4548703", "GSM4548704", "GSM4548705", "GSM4548706", "GSM4548707", "GSM4548708", "GSM4548709", "GSM4548710", "GSM4548711", "GSM4548712", "GSM4548713", "GSM4548714", "GSM4548715", "GSM4548716", "GSM4548717", "GSM4548718", "GSM4548719", "GSM4548720", "GSM4548721", "GSM4548722", "GSM4548723", "GSM4548724", "GSM4548725", "GSM4548726", "GSM4548727", "GSM4548728", "GSM4548729", "GSM4548730", "GSM4548731", "GSM4548732", "GSM4548733", "GSM4548734", "GSM4548735", "GSM4548736", "GSM4548737", "GSM4548738", "GSM4548739", "GSM4548740", "GSM4548741", "GSM4548742", "GSM4548743", "GSM4548744", "GSM4548745", "GSM4548746", "GSM4548747", "GSM4548748", "GSM4548749"], "sample_count": 59, "group_sizes": null, "group_sizes_basis": null, "platform": "21185", "taxon": "Homo sapiens", "title": "Identification of key genes potentially related to intervertebral disc degeneration by microarray analysis", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE150408 not downloaded", "asset:data:geo:GSE150408 licence not read"]}, "analysis": {"state": "partial", "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": "The “limma” package was used to screen DEIRGs between 17 healthy controls and 42 sciatica patients with the inclusion criteria log∣FC∣ > 0.2 and p < 0.001."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "Principal component analysis"}}, {"id": "method-4", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}, {"id": "method-5", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "support vector machine"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["GSE150408"], "resolved_accessions": ["GSE150408"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material. Further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE150408 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:34925462", "data:geo:GSE150408"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE150408"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:11:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9426, "completion_tokens": 1602, "cached_tokens": 256}}, "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:34925462", "type": "paper", "label": "pmid:34925462"}, {"id": "source:pmid:34925462", "type": "manuscript", "label": "PMID 34925462 full text"}, {"id": "data:geo:GSE150408", "type": "dataset", "label": "GEO GSE150408"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34925462", "type": "paper", "label": "pmid:34925462"}, {"id": "source:pmid:34925462", "type": "manuscript", "label": "PMID 34925462 full text"}, {"id": "data:geo:GSE150408", "type": "dataset", "label": "GEO GSE150408"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34925462", "type": "extraction", "used": ["source:pmid:34925462"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE150408", "type": "accession_resolution", "used": ["data:geo:GSE150408"], "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:34925462", "parent_hash": "sha256:02d3ea34cf39bc133cb1bed0309d303cd207cfab0a99618ea2cdae80a1ca5c65", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE150408 licence not read", "asset:data:geo:GSE150408 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["s by quantitative reverse transcription PCR (RT-qPCR). A diagnostic immune-related gene signature", "y quantitative reverse transcription PCR (RT-qPCR). A diagnostic immune-related gene signature", "ackage and verified in clinical specimens by quantitative reverse transcription PCR (RT-qPCR). A diagnostic immune-related gene", "ght healthy controls based on the results of RT-qPCR analysis. Spearman’s correlation analysis of"], "order_basis": "paper_text_order:603", "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": ["The “limma” package was used to screen DEIRGs between 17 healthy controls and 42 sciatica patients with the inclusion criteria log∣FC∣ > 0.2 and p < 0.001."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}