Identifying signature genes and their associations with immune cell infiltration in spinal cord injury.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39430218", "kind": "science-record", "revision": 3, "content_hash": "sha256:2e4cc17db54f28e7fd132dc4047796250e1dad723857b8c9eb8b70ee3ff34eb6", "created_at": "2026-11-01T20:29:40Z", "updated_at": "2026-11-01T22:12:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying signature genes and their associations with immune cell infiltration in spinal cord injury.", "doi": "10.1016/j.ibneur.2024.09.002", "pmid": "39430218", "authors": ["Meng Lv", "Yingjie Zhao", "Su'e Chang", "Zhengchao Gao"], "journal": "IBRO neuroscience reports", "year": 2024, "abstract": "Background: Early detection of spinal cord injury (SCI) is conducive to improving patient outcomes. In addition, many studies have revealed the role of immune cells in the progression or treatment of SCI. The objective of this study was to identify the early signature genes and clarify how they are related to immune cell infiltration in SCI.\nMethods: We analysed and identified early signature genes associated with SCI via bioinformatics analysis of the GSE151371 dataset from the GEO database. These genes were subsequently verified in the GSE33886 dataset and qRT-PCR. Finally, the CIBERSORT algorithm was used to examine the immune cell infiltration in SCI and its relationship with signature genes.\nResults: Seven SCI-related signature genes, including ARG1, RETN, BPI, GGH, CCNB1, HIST1H2AC, and HIST1H2BJ, were identified, and their expression was verified via an external validation cohort and qRT-PCR. Moreover, the ROC curves revealed the diagnostic value of these genes. In addition, on the basis of immune cell infiltration analysis, plasma cells, M0 macrophages, activated CD4+ memory T cells, γδ T cells, naive CD4+ T cells, and resting CD4+ memory T cells may participate in the progression of SCI.\nConclusion: This study identified seven early signature genes of SCI that may serve as biomarkers for the early diagnosis of SCI and contribute to our understanding of immune changes during the pathology of SCI.", "claims": [{"id": "claim-data-access", "statement": "Two datasets, namely GSE151371 and GSE33886, were downloaded from the Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo). The training dataset, GSE151371 include 38 SCI and 20 non-SCI blood samples, whereas the validation dataset, GSE33886, include 3 SCI and 4 non-SCI muscle samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39430218", "locator": "sections[3] \"Data sources and identification of DEGs\" paragraph 2", "quote": "Two datasets, namely GSE151371 and GSE33886, were downloaded from the Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo). The training dataset, GSE151371 include 38 SCI and 20 non-SCI blood samples, whereas the validation dataset, GSE33886, include 3 SCI and 4 non-SCI muscle samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Seven SCI-related signature genes—ARG1, RETN, BPI, GGH, CCNB1, HIST1H2AC, and HIST1H2BJ—were identified and validated as potential biomarkers for early diagnosis of SCI.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39430218", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Seven SCI-related signature genes, including ARG1, RETN, BPI, GGH, CCNB1, HIST1H2AC, and HIST1H2BJ, were identified, and their expression was verified via an external validation cohort and qRT—PCR."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Seven SCI-related signature genes—ARG1, RETN, BPI, GGH, CCNB1, HIST1H2AC, and HIST1H2BJ—were identified and validated as potential biomarkers for early diagnosis of SCI.", "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:39430218"], "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:GSE151371"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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:GSE151371"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39430218", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.ibneur.2024.09.002", "sha256": "sha256:9ea9d2b9fcf91915df26d53a46a902fc45912f93b9b73a3230592c9879efe3ff", "bytes": 28273, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.ibneur.2024.09.002", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11490871", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE151371", "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=GSE151371", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE151371", "version": null, "note": "Two datasets, namely GSE151371 and GSE33886, were downloaded from the Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo). 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