An alternative splicing signature in human Crohn's disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34749666", "kind": "science-record", "revision": 4, "content_hash": "sha256:9def37073c5b059ec34ee911f55c2e8bb68910cbed4aa782169bae9fb7f39483", "created_at": "2026-11-01T17:36:26Z", "updated_at": "2026-11-01T22:05:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An alternative splicing signature in human Crohn's disease.", "doi": "10.1186/s12876-021-02001-2", "pmid": "34749666", "authors": ["Daowei Li", "Yuanzi Liang", "Jia Lu", "Yue Tan"], "journal": "BMC gastroenterology", "year": 2021, "abstract": "BACKGROUND: Although hundreds of risk loci for Crohn's disease (CD) have been identified, the underlying pathogenesis of CD remains unclear. Recently, evidence has shown that aberrant gene expression in colon tissues of CD patients is associated with the progression of CD. We reasoned that post-transcriptional regulation, especially alternative splicing (AS), may also play important roles in the pathogenesis of CD.\nMETHODS: We re-analyzed public mRNA-seq data from the NCBI GEO dataset (GSE66207) and identified approximately 3000 unique AS events in CD patients compared to healthy controls.\nRESULTS: \"Lysine degradation\" and \"Sphingolipid metabolism\" were the two most enriched AS events in CD patients. In a validation study, we also sequenced eight subjects and demonstrated that key genes that were previously linked to CD, such as IRF1 and STAT3, also had significant AS events in CD.\nCONCLUSION: Our study provided a landscape of AS events in CD, especially as the first study focused on a Chinese cohort. Our data suggest that dysregulation of AS may be a new mechanism that contributes to the pathogenesis of CD.", "claims": [{"id": "claim-method", "statement": "To obtain differentially expressed AS events between Crohn’s disease patients and normal samples, we applied the Wilcoxon test on all AS events with at least three patients and one normal sample.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34749666", "locator": "sections[5] \"Identification of significant AS events\" paragraph 2", "quote": "To obtain differentially expressed AS events between Crohn’s disease patients and normal samples, we applied the Wilcoxon test on all AS events with at least three patients and one normal sample."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA-seq data for 20 CD AS anakysis was obtained from NCBI GEO dataset (GSE66207). “The datasets generated and/or analysed during the current study are available in the NCBI_GEO repository, [PERSISTENT WEB LINK OR ACCESSION NUMBER TO DATASETS]”.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34749666", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "RNA-seq data for 20 CD AS anakysis was obtained from NCBI GEO dataset (GSE66207). “The datasets generated and/or analysed during the current study are available in the NCBI_GEO repository, [PERSISTENT WEB LINK OR ACCESSION NUMBER TO DATASETS]”."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using MISO and related AS event analysis software on public GSE66207 RNA-seq data, the study identified approximately 3000 significant alternative splicing events in Crohn’s disease patients compared with controls.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34749666", "locator": "sections[1] \"Background\" paragraph 4", "quote": "Thus, we obtained public mRNA-seq data from the NCBI GEO dataset (GSE66207) [6], which included 33 colon tissue mRNA-seq data (20 CD and 13 healthy controls)."}, {"asset": "source:pmid:34749666", "locator": "sections[1] \"Background\" paragraph 4", "quote": "Using Mixture-of-Isoforms (MISO) and related AS event analysis software [15], we identified approximately 3000 significant AS events in CD patients compared in controls."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using MISO and related AS event analysis software on public GSE66207 RNA-seq data, the study identified approximately 3000 significant alternative splicing events in Crohn’s disease patients compared with controls.", "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:34749666"], "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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