Aberrantly methylated-differentially expressed genes and related pathways in cholangiocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35758372", "kind": "science-record", "revision": 4, "content_hash": "sha256:0582d58dd5d6fd32b3d734853a94cd9d5997c1b84393788d6469dff406ec7f59", "created_at": "2026-11-01T18:14:47Z", "updated_at": "2026-11-01T22:06:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Aberrantly methylated-differentially expressed genes and related pathways in cholangiocarcinoma.", "doi": "10.1097/MD.0000000000029379", "pmid": "35758372", "authors": ["Guan Lin", "Zhang Xinhe", "Tian Haoyu", "Li Yiling"], "journal": "Medicine", "year": 2022, "abstract": "ABSTRACT: This study aimed to explore aberrantly methylated-differentially expressed genes and related pathways in cholangiocarcinoma (CCA).The mRNA expression data (GSE26566) and methylation profiling data (GSE44965) were collected from the Gene Expression Omnibus (GEO) Datasets. Differentially expressed genes and differentially methylated genes were identified using GEO2R. Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using clusterprofiler in R. MCODE clustering tool was used to screen modules of the protein-protein interaction network in Cytoscape. Related pathways of hub gene by using gene set enrichment analysis.Eighty-one hypermethylated, lowly expressed genes (Hyper-LGs) and 76 hypomethylated, highly expressed genes (Hypo-HGs) were identified in this study. Hyper-LGs were enriched in ion channel binding and transcription factor activity, which was associated with Mineral absorption and Cell adhesion molecules. Hypo-HGs were enriched in cysteine-type endopeptidase activity, which was associated with Sphingolipid signaling pathway and T cell receptor signaling pathway. Based on protein-protein interaction networks, MYC and VWF were identified as hub genes for Hyper-LGs, and no hub genes for Hypo-HGs.This study found methylated-differentially expressed genes and signaling pathways that are connected with the CCA by using a series of bioinformatics databases and tools. MYC and VWF act as hub genes of CCA, which can be used as biomarkers based on aberrant methylation for the accurate diagnosis and treatment of CCA.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes and differentially methylated genes were identified using GEO2R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35758372", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed genes and differentially methylated genes were identified using GEO2R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during and/or analyzed during the current study are available in the Gene Expression Omnibus (GEO) Datasets repository, (https://www.ncbi.nlm.nih.gov/gds/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35758372", "locator": "sections[19] \"Footnotes\" paragraph 2", "quote": "The datasets generated during and/or analyzed during the current study are available in the Gene Expression Omnibus (GEO) Datasets repository, (https://www.ncbi.nlm.nih.gov/gds/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 81 hypermethylated, lowly expressed genes and 76 hypomethylated, highly expressed genes, with MYC and VWF identified as hub genes for the Hyper-LGs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35758372", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Eighty-one hypermethylated, lowly expressed genes (Hyper-LGs) and 76 hypomethylated, highly expressed genes (Hypo-HGs) were identified in this study."}, {"asset": "source:pmid:35758372", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Based on protein–protein interaction networks, MYC and VWF were identified as hub genes for Hyper-LGs, and no hub genes for Hypo-HGs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 81 hypermethylated, lowly expressed genes and 76 hypomethylated, highly expressed genes, with MYC and VWF identified as hub genes for the Hyper-LGs.", "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:35758372"], "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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