A bioinformatics approach to systematically analyze the molecular patterns of monkeypox virus-host cell interactions.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38737277", "kind": "science-record", "revision": 5, "content_hash": "sha256:6157f5c3d6ddc8b7b42b1dbba6b02a4e2cdbf8636648b822eb89ce593f281676", "created_at": "2026-11-01T19:20:42Z", "updated_at": "2026-11-01T22:54:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A bioinformatics approach to systematically analyze the molecular patterns of monkeypox virus-host cell interactions.", "doi": "10.1016/j.heliyon.2024.e30483", "pmid": "38737277", "authors": ["Zhongxiang Tang", "Ying Han", "Yuting Meng", "Jiani Li", "Xiangjie Qiu", "Ousman Bajinka", "Guojun Wu", "Yurong Tan"], "journal": "Heliyon", "year": 2024, "abstract": "Monkeypox has been spreading worldwide since May 2022, when the World Health Organization (WHO) declared the outbreak a \"public health emergency of international concern.\" The spread of monkeypox has posed a serious threat to the health of people around the world, but few studies have been conducted, and the molecular mechanism of monkeypox after infection remains unclear. We therefore implemented a transcriptome analysis to identify signaling pathways and biomarkers in monkeypox-infected cells to help understand monkeypox-host cell interactions. In this study, datasets GSE36854 and GSE11234 were obtained from GEO. Of these, 84 significantly different genes were identified in the dataset GSE36854, followed by KEGG, GO analysis protein-protein interaction (PPI) construction, and Hub gene extraction. We also analyzed the expression regulation of hub genes and screened for drugs targeting hub genes. The results showed that monkeypox-infected cells significantly activated the cellular immune response. The top 10 hub genes are IER3, IFIT2, IL11, ZC3H12A, EREG, IER2, NFKBIE, FST, IFIT1 and AREG. AP-26113 and itraconazole can be used to counteract the inhibitory effect of monkeypox on IFIT1 and IFIT2 and serve as candidate drugs for the treatment of monkeypox virus infection. IRF1 may also be a transcription factor of IFIT. Our results provide a new entry point for understanding how monkeypox virus interacts with its host.", "claims": [{"id": "claim-method", "statement": "We processed and visualized sequence data using R (R version 4.1.3) language in which the Limma package was used to screen for significantly differentially expressed genes [18].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38737277", "locator": "sections[4] \"Acquisition of sequencing data and differential gene analysis\" paragraph 2", "quote": "We processed and visualized sequence data using R (R version 4.1.3) language in which the Limma package was used to screen for significantly differentially expressed genes [18]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38737277", "locator": "sections[21] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The results showed that monkeypox-infected cells significantly activated the cellular immune response.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38737277", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The results showed that monkeypox-infected cells significantly activated the cellular immune response."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The results showed that monkeypox-infected cells significantly activated the cellular immune response.", "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:38737277"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE11234"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE11234"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38737277", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e30483", "sha256": "sha256:22cdf5ebee8e38f6afa3d20481cb8a42985577c6aec434ca25664707e40f545a", "bytes": 47904, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e30483", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11088324", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE11234", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11234", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE11234", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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