Integrated machine learning and Mendelian randomization reveal PALMD as a prognostic biomarker for nonspecific orbital inflammation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39402101", "kind": "science-record", "revision": 4, "content_hash": "sha256:3f0ddb1b225c8cb964445aa2f6c3f69e124a8c7879a2e2d51456a22e1682c355", "created_at": "2026-11-01T20:29:38Z", "updated_at": "2026-11-01T22:55:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated machine learning and Mendelian randomization reveal PALMD as a prognostic biomarker for nonspecific orbital inflammation.", "doi": "10.1038/s41598-024-74409-1", "pmid": "39402101", "authors": ["Zixuan Wu", "Xiaohua Liu", "Kang Tan", "Xiaolei Yao", "Qinghua Peng"], "journal": "Scientific reports", "year": 2024, "abstract": "BACKGROUND: Nonspecific Orbital Inflammation (NSOI) remains a perplexing enigma among proliferative inflammatory disorders. Its etiology is idiopathic, characterized by distinctive and polymorphous lymphoid infiltration within the orbital region. Preliminary investigations suggest that PALMD localizes within the cytosol, potentially playing a crucial role in cellular processes, including plasma membrane dynamics and myogenic differentiation. The potential of PALMD as a biomarker for NSOI warrants meticulous exploration.\nMETHODS: PALMD was identified through the intersection analysis of common DEGs from datasets GSE58331 and GSE105149 from the GEO database, alongside immune-related gene lists from the ImmPort database, using Lasso regression and SVM-RFE analysis. GSEA and GSVA were conducted with gene sets co-expressed with PALMD. To further investigate the correlation between PALMD and immune-related biological processes, the CIBERSORT algorithm and ESTIMATE method were employed to evaluate immune microenvironment characteristics of each sample. The expression levels of PALMD were subsequently validated using GSE105149.\nRESULTS: Among the 314 DEGs identified, several showed significant differences. Lasso and SVM-RFE algorithms pinpointed 15 hub genes. Functional analysis of PALMD emphasized its involvement in cell-cell adhesion, leukocyte migration, and leukocyte-mediated immunity. Enrichment analysis revealed that gene sets positively correlated with PALMD were enriched in immune-related pathways. Immune infiltration analysis indicated that resting dendritic cells, resting mast cells, activated NK cells, and plasma cells positively associate with PALMD expression. Conversely, naive B cells, activated dendritic cells, M0 and M1 macrophages, activated mast cells, activated CD4 memory T cells, and naive CD4 T cells showed a negative correlation with PALMD expression. PALMD demonstrated significant diagnostic potential in differentiating NSOI.\nCONCLUSIONS: This study identifies PALMD as a potential biomarker linked to NSOI, providing insights into its pathogenesis and offering new avenues for tracking disease progression.", "claims": [{"id": "claim-method", "statement": "Differential expression analyses between NSOI and control groups were conducted utilizing the Linear Models for Microarray Data (limma) package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39402101", "locator": "sections[3] \"Transcriptional profiling data and determination of differentially expressed genes (DEGs)\" paragraph 2", "quote": "Differential expression analyses between NSOI and control groups were conducted utilizing the Linear Models for Microarray Data (limma) package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are available in the appendix. Thanks to the KEGG database for the great support43. The citation guidelines: www.kegg.jp/kegg/kegg1.html.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39402101", "locator": "sections[24] \"notes\" paragraph 1", "quote": "The datasets generated during and/or analyzed during the current study are available in the appendix. Thanks to the KEGG database for the great support43. The citation guidelines: www.kegg.jp/kegg/kegg1.html."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using limma on GEO datasets GSE58331 and GSE105149, the study identified 314 differentially expressed genes and 15 hub genes, including PALMD, which demonstrated diagnostic potential for differentiating NSOI.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39402101", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "PALMD was identified through the intersection analysis of common DEGs from datasets GSE58331 and GSE105149 from the GEO database, alongside immune-related gene lists from the ImmPort database, using Lasso regression and SVM-RFE analysis."}, {"asset": "source:pmid:39402101", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Among the 314 DEGs identified, several showed significant differences."}, {"asset": "source:pmid:39402101", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "PALMD demonstrated significant diagnostic potential in differentiating NSOI."}, {"asset": "source:pmid:39402101", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "This study identifies PALMD as a potential biomarker linked to NSOI, providing insights into its pathogenesis and offering new avenues for tracking disease progression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using limma on GEO datasets GSE58331 and GSE105149, the study identified 314 differentially expressed genes and 15 hub genes, including PALMD, which demonstrated diagnostic potential for differentiating NSOI.", "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:39402101"], "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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