Bioinformatic analysis identified novel candidate genes with the potentials for diagnostic blood testing of primary biliary cholangitis.

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Diagnosis of PBC is generally based on the existence of anti-mitochondrial antibody (AMA) in blood samples; however, some PBC patients are negative for serum AMA tests, and invasive liver histological testing is required in rare PBC cases. The current study seeks novel candidate genes that are associated with PBC status and have potentials for blood diagnostic testing. Human transcriptomic profiling data of liver and blood samples were obtained from Gene Expression Omnibus (GEO). Three GEO data series (GSE79850, GSE159676, and GSE119600) were downloaded, and bioinformatic analyses were performed. Various differentially expressed genes were identified in three data series by comparing PBC patients and control individuals. Twelve candidate genes were identified, which were upregulated in both liver tissues and blood samples of PBC patients in all three data series. The enrichment analysis demonstrated that 8 out of 12 candidate genes were associated with biological functions, which were closely related to autoimmune diseases including PBC. Candidate genes, especially ITGAL showed good potentials to distinguish PBC with other diseases. These candidate genes could be useful for diagnostic blood testing of PBC, although further clinical studies are required to evaluate their potentials as diagnostic biomarkers.", "claims": [{"id": "claim-method", "statement": "DEGs comparing control and PBC groups in three data series were identified using the limma package [18].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37844121", "locator": "sections[5] \"Identification of differentially expressed genes (DEGs)\" paragraph 2", "quote": "DEGs comparing control and PBC groups in three data series were identified using the limma package [18]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Twelve candidate genes were identified, which were upregulated in both liver tissues and blood samples of PBC patients in all three data series.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37844121", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Twelve candidate genes were identified, which were upregulated in both liver tissues and blood samples of PBC patients in all three data series."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Twelve candidate genes were identified, which were upregulated in both liver tissues and blood samples of PBC patients in all three data series.", "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:37844121"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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