Screening of underlying genetic biomarkers for ankylosing spondylitis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31059041", "kind": "science-record", "revision": 8, "content_hash": "sha256:e2c6fcdb8e0b2d07a0d92e67edfb1dd9fdf01d3819317291af44237312f74fd8", "created_at": "2026-11-01T15:40:44Z", "updated_at": "2026-11-01T22:43:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening of underlying genetic biomarkers for ankylosing spondylitis.", "doi": "10.3892/mmr.2019.10188", "pmid": "31059041", "authors": ["Xutao Fan", "Bao Qi", "Longfei Ma", "Fengyu Ma"], "journal": "Molecular medicine reports", "year": 2019, "abstract": "Genetic biomarkers for the diagnosis of ankylosing spondylitis (AS) remain unreported except for human leukocyte antigen B27 (HLA‑B27). Therefore, the aim of the present study was to screen the differentially expressed genes (DEGs), and those that also possess differential single nucleotide polymorphism (SNP) loci in the whole blood of AS patients compared with healthy controls by integrating two mRNA expression profiles (GSE73754 and GSE25101) and SNP microarray data (GSE39428) collected from the Gene Expression Omnibus (GEO). Using the t‑test, 1,056 and 1,073 DEGs were identified in the GSE73754 and GSE25101 datasets, respectively. Among them, 234 DEGs were found to be shared in both datasets, which were subsequently overlapped with 122 differential SNPs of genes in the GSE39428 dataset, resulting in identification of two common genes [eukaryotic translation elongation factor 1 epsilon 1 (EEF1E1) and serpin family A member 1 (SERPINA1)]. Their expression levels were significantly upregulated and the average expression log R ratios of SNP sites in these genes were significantly higher in AS patients than those in controls. Function enrichment analysis revealed that EEF1E1 was involved in AS by influencing the aminoacyl‑tRNA biosynthesis, while SERPINA1 may be associated with AS by participating in platelet degranulation. However, only the genotype and allele frequencies of SNPs (rs7763907 and rs7751386) in EEF1E1 between AS and controls were significantly different between AS and the controls, but not SERPINA1. These findings suggest that EEF1E1 may be an underlying genetic biomarker for the diagnosis of AS.", "claims": [{"id": "claim-method", "statement": "The DEGs between control and AS in the GSE73754 and GSE25101 datasets were identified using the LIMMA method (22) based on the t-test where statistical significance was set to |logFC(fold change)| >0.263 and Benjamini and Hochberg adjusted (24) false discovery rate (FDR) <0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31059041", "locator": "sections[6] \"Differential analysis of mRNAs and SNPs\" paragraph 2", "quote": "The DEGs between control and AS in the GSE73754 and GSE25101 datasets were identified using the LIMMA method (22) based on the t-test where statistical significance was set to |logFC(fold change)| >0.263 and Benjamini and Hochberg adjusted (24) false discovery rate (FDR) <0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data GSE73754 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73754), GSE25101 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25101) and GSE39428 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39428) were downloaded from the GEO database in NCBI.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31059041", "locator": "sections[18] \"Availability of data and materials\" paragraph 2", "quote": "The microarray data GSE73754 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73754), GSE25101 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25101) and GSE39428 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39428) were downloaded from the GEO database in NCBI."}], "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:31059041"], "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:GSE25101"], "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:GSE25101"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31059041", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/mmr.2019.10188", "sha256": 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(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25101) and GSE39428 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39428) were downloaded from the GEO database in NCBI.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray data GSE73754 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73754), GSE25101 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25101) and GSE39428 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE39428) were downloaded from the GEO database in NCBI.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM616668", "GSM616669", "GSM616670", "GSM616671", "GSM616672", "GSM616673", "GSM616674", "GSM616675", "GSM616676", "GSM616677", "GSM616678", "GSM616679", "GSM616680", "GSM616681", "GSM616682", "GSM616683", "GSM616684", "GSM616685", "GSM616686", "GSM616687", "GSM616688", "GSM616689", "GSM616690", "GSM616691", "GSM616692", "GSM616693", 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