Screening the hub genes and analyzing the mechanisms in discharged COVID-19 patients retesting positive through bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35657140", "kind": "science-record", "revision": 4, "content_hash": "sha256:35a65e3a3ac9a24fe2446139d1d427d95d0d193fa4191209e9434f2ca57c2da6", "created_at": "2026-11-01T18:14:36Z", "updated_at": "2026-11-01T22:06:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Screening the hub genes and analyzing the mechanisms in discharged COVID-19 patients retesting positive through bioinformatics analysis.", "doi": "10.1002/jcla.24495", "pmid": "35657140", "authors": ["Ke-Ying Fang", "Gui-Ning Liang", "Zhuo-Qing Zhuang", "Yong-Xin Fang", "Yu-Qian Dong", "Chuang-Jia Liang", "Xin-Yan Chen", "Xu-Guang Guo"], "journal": "Journal of clinical laboratory analysis", "year": 2022, "abstract": "BACKGROUND: After encountering COVID-19 patients who test positive again after discharge, our study analyzed the pathogenesis to further assess the risk and possibility of virus reactivation.\nMETHODS: A separate microarray was acquired from the Gene Expression Omnibus (GEO), and its samples were divided into two groups: a \"convalescent-RTP\" group consisting of convalescent and \"retesting positive\" (RTP) patients (group CR) and a \"healthy-RTP\" group consisting of healthy control and RTP patients (group HR). The enrichment analysis was performed with R software, obtaining the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Subsequently, the protein-protein interaction (PPI) networks of each group were established, and the hub genes were discovered using the cytoHubba plugin.\nRESULTS: In this study, 6622 differentially expressed genes were identified in the group CR, among which RAB11B-AS1, DISP1, MICAL3, PSMG1, and DOCK4 were up-regulated genes, and ANAPC1, IGLV1-40, SORT1, PLPPR2, and ATP1A1-AS1 were down-regulated. 7335 genes were screened in the group HR, including the top 5 up-regulated genes ALKBH6, AMBRA1, MIR1249, TRAV18, and LRRC69, and the top 5 down-regulated genes FAM241B, AC018529.3, AL031963.3, AC006946.1, and FAM149B1. The GO and KEGG analysis of the two groups revealed a significant enrichment in immune response and apoptosis. In the PPI network constructed, group CR and group HR identified 10 genes, respectively, and TP53BP1, SNRPD1, and SNRPD2 were selected as hub genes.\nCONCLUSIONS: Using the messenger ribonucleic acid (mRNA) expression data from GSE166253, we found TP53BP1, SNRPD1, and SNRPD2 as hub genes in RTP patients, which is vital to the management and prognostic prediction of RTP patients.", "claims": [{"id": "claim-method", "statement": "Downloading the GSE166253 dataset from the GEO database, we conducted differential expression analysis using the R language.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35657140", "locator": "sections[8] \"Screening of DEGs\" paragraph 2", "quote": "Downloading the GSE166253 dataset from the GEO database, we conducted differential expression analysis using the R language."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE166253 dataset that support the findings of this study are openly available in GEO database at https://www.ncbi.nlm.nih.gov/gds/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35657140", "locator": "sections[17] \"DATA AVAILABILITY STATEMENT\" paragraph 2", "quote": "The GSE166253 dataset that support the findings of this study are openly available in GEO database at https://www.ncbi.nlm.nih.gov/gds/."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In the PPI network constructed, group CR and group HR identified 10 genes, respectively, and TP53BP1, SNRPD1, and SNRPD2 were selected as hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35657140", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In the PPI network constructed, group CR and group HR identified 10 genes, respectively, and TP53BP1, SNRPD1, and SNRPD2 were selected as hub genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In the PPI network constructed, group CR and group HR identified 10 genes, respectively, and TP53BP1, SNRPD1, and SNRPD2 were selected as hub genes.", "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:35657140"], "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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