Key regulatory genes and signaling pathways involved in islet culture: a bioinformatic analysis.

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This study aimed to track out hub genes and pathways in the process of islet culture by bioinformatic analysis. We downloaded the gene expression microarray of GSE42591 from the Gene Expression Omnibus (GEO). Aberrant Differentially methylated genes (DMGs) were obtained using the GEO2R tool. Gene ontology (GO) analysis and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analyses were performed on selected genes by using the Database for Annotation Visualization and Integrated Discovery (DAVID). A protein-protein interaction (PPI) network was constructed with the Retrieval of Interacting Genes (STRING) and visualized in Cytoscape 3.7.2. A total of 434 genes were overexpressed and 114 genes underexpressed in fresh to cultured 4 h tissue. KEGG pathway enrichment analyses revealed the TGF-beta signaling pathway, MAPK signaling pathway, or VEGF signaling pathway. The genes FN1, MKI67, IGF1, MAPK14, COL1A1 might be involved in islet culture. In general, this work scrutinized islet culture-relevant knowledge and provided insight into the regulation and mediation of islet survival.", "claims": [{"id": "claim-method", "statement": "Aberrant Differentially methylated genes (DMGs) were obtained using the GEO2R tool.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33564361", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Aberrant Differentially methylated genes (DMGs) were obtained using the GEO2R tool."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded the gene expression microarray of GSE42591 from the Gene Expression Omnibus (GEO).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33564361", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We downloaded the gene expression microarray of GSE42591 from the Gene Expression Omnibus (GEO)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Bioinformatic analysis identified 434 overexpressed and 114 underexpressed genes in fresh to cultured 4 h tissue and implicated FN1, MKI67, IGF1, MAPK14, and COL1A1 in islet culture.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:33564361", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 434 genes were overexpressed and 114 genes underexpressed in fresh to cultured 4 h tissue."}, {"asset": "source:pmid:33564361", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The genes FN1, MKI67, IGF1, MAPK14, COL1A1 might be involved in islet culture."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "complete", "objective": "Bioinformatic analysis identified 434 overexpressed and 114 underexpressed genes in fresh to cultured 4 h tissue and implicated FN1, MKI67, IGF1, MAPK14, and COL1A1 in islet culture.", "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:33564361"], "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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