Identification of the Hub Genes and the Signaling Pathways in Human iPSC-Cardiomyocytes Infected by SARS-CoV-2.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35235083", "kind": "science-record", "revision": 6, "content_hash": "sha256:e68e4758b4c081d4a266f4671d50f1e87c0fc95520c73536002397600ec3cd32", "created_at": "2026-11-01T17:36:59Z", "updated_at": "2026-11-01T22:48:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the Hub Genes and the Signaling Pathways in Human iPSC-Cardiomyocytes Infected by SARS-CoV-2.", "doi": "10.1007/s10528-022-10206-7", "pmid": "35235083", "authors": ["Li-Min Xie", "Yin-Fei Huang", "Ye-Ling Liu", "Jia-Qi Liang", "Wei Deng", "Geng-Ling Lin", "Huan-Min Luo", "Xu-Guang Guo"], "journal": "Biochemical genetics", "year": 2022, "abstract": "Severe Acute Respiratory Syndrome Coronavirus Type 2 (SARS-CoV-2) is an enveloped single-stranded RNA virus that can lead to respiratory symptoms and damage many organs such as heart, kidney, intestine, brain and liver. It has not been clearly documented whether myocardial injury is caused by direct infection of cardiomyocytes, lung injury, or other unknown mechanisms. The gene expression profile of GSE150392 was obtained from the Gene Expression Omnibus (GEO) database. The processing of high-throughput sequencing data and the screening of differentially expressed genes (DEGs) were implemented by R software. The R software was employed to analyze the Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The protein-protein interaction (PPI) network of the DEGs was constructed by the STRING website. The Cytoscape software was applied for the visualization of PPI network and the identification of hub genes. The statistical analysis was performed by the GraphPad Prism software to verify the hub genes. A total of 516 up-regulated genes and 191 down-regulated genes were screened out. The top 1 enrichment items of GO in biological process (BP), Cellular Component (CC), and Molecular Function (MF) were type I interferon signaling pathway, sarcomere, and receptor ligand activity, respectively. The top 10 enrichment pathways, including TNF signaling pathway, were identified by KEGG enrichment analysis. A PPI network was established, consisting of 613 nodes and 3,993 edges. The 12 hub genes were confirmed as statistically significant, which was verified by GSE151879 dataset. In conclusion, the hub genes of human iPSC-cardiomyocytes infected with SARS-CoV-2 were identified through bioinformatics analysis, which may be used as biomarkers for further research.", "claims": [{"id": "claim-method", "statement": "The limma package of the R software was employed to screen differentially expressed genes (DEGs) with conditions of |log2FC|≥ 2 and P < 0.05, the pheatmap package to construct the heat-map of DEGs, and the ggplot2 package (Ito and Murphy 2013) to construct the volcano map.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35235083", "locator": "sections[4] \"Data Processing\" paragraph 2", "quote": "The limma package of the R software was employed to screen differentially expressed genes (DEGs) with conditions of |log2FC|≥ 2 and P < 0.05, the pheatmap package to construct the heat-map of DEGs, and the ggplot2 package (Ito and Murphy 2013) to construct the volcano map."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35235083", "locator": "sections[18] \"Data availability\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 707 differentially expressed genes, including 516 up-regulated and 191 down-regulated genes, using GSE150392.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Totally 707 DEGs have been screened out according to the criteria of |log2FC|≥ 2 and P < 0.05, including 516 up-regulated genes and 191 down-regulated genes, the results of which were presented in the form of volcano map and heat map (Fig. 1A, B) with the help of ggplot2 package and pheatmap package in the R software."}, "evidence": [{"asset": "source:pmid:35235083", "locator": "sections[9] \"Identification of DEGs\" paragraph 2", "quote": "Totally 707 DEGs have been screened out according to the criteria of |log2FC|≥ 2 and P < 0.05, including 516 up-regulated genes and 191 down-regulated genes, the results of which were presented in the form of volcano map and heat map (Fig. 1A, B) with the help of ggplot2 package and pheatmap package in the R software."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 707 differentially expressed genes, including 516 up-regulated and 191 down-regulated genes, using GSE150392.", "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:35235083"], "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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