WGCNA and machine learning analysis identifi ed SAMD9 and IFIT3 as primary Sjögren's Syndrome key genes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38707449", "kind": "science-record", "revision": 5, "content_hash": "sha256:8d88d461413094766278957a95deb8c4f3c32ec4f1320e83c60554b6a594cb28", "created_at": "2026-11-01T19:20:40Z", "updated_at": "2026-11-01T22:54:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "WGCNA and machine learning analysis identifi ed SAMD9 and IFIT3 as primary Sjögren's Syndrome key genes.", "doi": "10.1016/j.heliyon.2024.e29652", "pmid": "38707449", "authors": ["Shu Liu", "Hongzhen Chen", "Lin Tang", "Mian Liu", "Jinfeng Chen", "Dandan Wang"], "journal": "Heliyon", "year": 2024, "abstract": "Background: Current treatments for primary Sjögren's Syndrome (pSS) are with limited effect, partially due to the heterogeneity and uncleared mechanism.\nMethods: We got GSE40568 (Japan) and GSE40611 (USA), and analyzed them with WGCNA to find key Differentially expressed genes (DEGs) between pSS and healthy salivary glands (SG). Key pSS genes (KPGs) were further selected through 3 machine-learning methods. The expression of KPGs was validated via two other GEO datasets (GSE127952 and GSE154926). Infiltrated immune cells, ceRNA network, and potential compounds were explored.\nResults: Our study identified 376 DEGs from the pSS patients, with 186 genes located in the \"plum2\" module, showing the strongest correlation with clinical characteristics. SAMD9 and IFIT3 emerged as KPGs with excellent diagnostic potential. SAMD9 demonstrated close association with immune cell infiltration. We constructed a lncRNA-miRNA-mRNA network comprising 2 KPGs, 12 miRNAs, 124 lncRNAs, and potential therapeutic targets.\nConclusion: In the investigation of pSS public datasets, our study revealed two potential critical mediators in the pathological process of pSS salivary glands, namely SAMD9 and IFIT3. Furthermore, we put forth a hypothesis regarding the ceRNA network and made predictions regarding potential therapeutic drugs targeting these two genes.", "claims": [{"id": "claim-method", "statement": "Differential gene analysis (DEGs) between the samples pSS patient and control individuals was carried out by using the “limma” package [10], with an adjusted P value < 0.05 and a |log2 fold change| > 1 as the criteria for detecting DEGs in the dataset comparing diseased and control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38707449", "locator": "sections[4] \"Exploration of the key genes for pSS\" paragraph 2", "quote": "Differential gene analysis (DEGs) between the samples pSS patient and control individuals was carried out by using the “limma” package [10], with an adjusted P value < 0.05 and a |log2 fold change| > 1 as the criteria for detecting DEGs in the dataset comparing diseased and control samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data used in this study are publicly available downloaded from GSE40568, GSE40611, GSE127952 and GSE154926 in GEO database without any access restrictions, and the analyzed scripts by R software are available upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38707449", "locator": "sections[10] \"Data availability statement\" paragraph 2", "quote": "All data used in this study are publicly available downloaded from GSE40568, GSE40611, GSE127952 and GSE154926 in GEO database without any access restrictions, and the analyzed scripts by R software are available upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified SAMD9 and IFIT3 as two potential critical mediators in the pathological process of pSS salivary glands.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38707449", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "In the investigation of pSS public datasets, our study revealed two potential critical mediators in the pathological process of pSS salivary glands, namely SAMD9 and IFIT3."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified SAMD9 and IFIT3 as two potential critical mediators in the pathological process of pSS salivary glands.", "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:38707449"], "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:GSE127952"], "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:GSE127952"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38707449", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e29652", "sha256": 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