Integrating Transcriptomics and Machine Learning to Uncover the FLI1-PARP14-Immune Axis in Ulcerative Colitis Activity and Pathogenesis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41300794", "kind": "science-record", "revision": 3, "content_hash": "sha256:adae8410ca7b1a86ec2a932b543d09b46b45d8ac56c9187600fcd828711fdfb8", "created_at": "2026-11-01T20:31:19Z", "updated_at": "2026-11-01T22:15:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrating Transcriptomics and Machine Learning to Uncover the FLI1-PARP14-Immune Axis in Ulcerative Colitis Activity and Pathogenesis.", "doi": "10.3390/genes16111342", "pmid": "41300794", "authors": ["Zhizhong Zheng", "Yayu Zhang", "Zhixing Gao", "Houyu Chen", "Gang Song"], "journal": "Genes", "year": 2025, "abstract": "Background: Ulcerative colitis (UC) is a chronic inflammatory bowel disease whose molecular mechanisms of action remain incompletely characterized. This study was designed to develop potential diagnostic biomarkers and unravel the pathogenic causes of UC activity through the integration of transcriptome analysis with machine learning and genetic causal inference. Methods: Gene expression datasets (GSE75214, GSE53306, GSE179285) from the GEO database were evaluated. Weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) analysis were applied to discover activity-associated genes. Protein-protein interaction networks and ensemble machine learning methods were utilized to refine the potential list. Furthermore, summary-data-based Mendelian Randomization (SMR) analysis and immune infiltration research were conducted. Results: Eight characteristic genes were identified, with CXCL11, PARP14, and IFITM1 emerging as hub genes. These hub genes exhibited strong diagnostic accuracy, with consistent area under the curve (AUC) values exceeding 0.83 across 3 independent cohorts. SMR analysis demonstrated a probable causal connection between higher PARP14 and UC susceptibility. The hub genes were strongly correlated with immune cells, including M1 macrophages and NK cells. FLI1 was discovered as a critical upstream transcription factor regulating this network. Conclusions: The findings outline a FLI1-PARP14-immune axis central to UC activity, providing unique insights into its pathophysiology and highlighting PARP14 as a promising diagnostic biomarker and potential therapeutic target.", "claims": [{"id": "claim-method", "statement": "To evaluate potential causal relationships between gene expression and UC susceptibility, summary-data–based Mendelian randomization (SMR) analysis [30] was conducted.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41300794", "locator": "sections[11] \"2.9. Summary-Data–Based Mendelian Randomization (SMR) Analysis\" paragraph 2", "quote": "To evaluate potential causal relationships between gene expression and UC susceptibility, summary-data–based Mendelian randomization (SMR) analysis [30] was conducted."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA expression dataset is publicly accessible through the NCBI GEO repository at https://www.ncbi.nlm.nih.gov/geo/ (accessed on 5 August 2025). All findings from this research have been incorporated into the manuscript. Additional data can be obtained by contacting the corresponding author with a formal request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41300794", "locator": "sections[30] \"notes\" paragraph 1", "quote": "The RNA expression dataset is publicly accessible through the NCBI GEO repository at https://www.ncbi.nlm.nih.gov/geo/ (accessed on 5 August 2025). All findings from this research have been incorporated into the manuscript. Additional data can be obtained by contacting the corresponding author with a formal request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:41300794"], "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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