Identification of hub genes and key pathways in arsenic-treated rice (Oryza sativa L.) based on 9 topological analysis methods of CytoHubba.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39111872", "kind": "science-record", "revision": 4, "content_hash": "sha256:a164c7d3a0a528c7f971b08db816d73a867c24aa8aeb19192f2f4f83d1a3ef53", "created_at": "2026-11-01T20:29:12Z", "updated_at": "2026-11-01T22:54:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes and key pathways in arsenic-treated rice (Oryza sativa L.) based on 9 topological analysis methods of CytoHubba.", "doi": "10.1265/ehpm.24-00095", "pmid": "39111872", "authors": ["Zhen Yu", "Rongxuan Wang", "Tian Dai", "Yuan Guo", "Zanxuan Tian", "Yuanyuan Zhu", "Juan Chen", "Yongjian Yu"], "journal": "Environmental health and preventive medicine", "year": 2024, "abstract": "BACKGROUND: Arsenic is a toxic metalloid that can cause acute and chronic adverse health problems. Unfortunately, rice, the primary staple food for more than half of the world's population, is generally regarded as a typical arsenic-accumulating crop plant. Evidence indicates that arsenic stress can influence the growth and development of the rice plant, and lead to high concentrations of arsenic in rice grain. But the underlying mechanisms remain unclear.\nMETHODS: In the present research, the possible molecules and pathways involved in rice roots in response to arsenic stress were explored using bioinformatics methods. Datasets that involving arsenic-treated rice root and the \"study type\" that was restricted to \"Expression profiling by array\" were selected and downloaded from Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between the arsenic-treated group and the control group were obtained using the online web tool GEO2R. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed to investigate the functions of DEGs. The protein-protein interactions (PPI) network and the molecular complex detection algorithm (MCODE) of DEGs were analyzed using STRING and Cystoscope, respectively. Important nodes and hub genes in the PPI network were predicted and explored using the Cytoscape-cytoHubba plug-in.\nRESULTS: Two datasets, GSE25206 and GSE71492, were downloaded from Gene Expression Omnibus (GEO) database. Eighty common DEGs from the two datasets, including sixty-three up-regulated and seventeen down-regulated genes, were then selected. After functional enrichment analysis, these common DEGs were enriched mainly in 10 GO items, including glutathione transferase activity, glutathione metabolic process, toxin catabolic process, and 7 KEGG pathways related to metabolism. After PPI network and MCODE analysis, 49 nodes from the DEGs PPI network were identified, filtering two significant modules. Next, the Cytoscape-cytoHubba plug-in was used to predict important nodes and hub genes. Finally, five genes [Os01g0644000, PRDX6 (Os07g0638400), PRX112 (Os07g0677300), ENO1(Os06g0136600), LOGL9 (Os09g0547500)] were verified and could serve as the best candidates associated with rice root in response to arsenic stress.\nCONCLUSIONS: In summary, we elucidated the potential pathways and genes in rice root in response to arsenic stress through a comprehensive bioinformatics analysis.", "claims": [{"id": "claim-method", "statement": "The online web tool, GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), is often used to explore the genetic variations between two or more groups of samples based on the GEOquery and Limma R packages [31].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39111872", "locator": "sections[4] \"2.2 Differentially expressed genes identification\" paragraph 2", "quote": "The online web tool, GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), is often used to explore the genetic variations between two or more groups of samples based on the GEOquery and Limma R packages [31]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression profiles datasets used in this study are publicly available at GEO database (https://www.ncbi.nlm.nih.gov/geo/): GSE25206, GSE99083, and GSE71492.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39111872", "locator": "sections[19] \"Availability of data and materials\" paragraph 2", "quote": "The expression profiles datasets used in this study are publicly available at GEO database (https://www.ncbi.nlm.nih.gov/geo/): GSE25206, GSE99083, and GSE71492."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using GEO2R on the GEO expression profiles GSE25206 and GSE71492, the study identified 80 common differentially expressed genes and nominated five hub genes associated with rice-root responses to arsenic stress.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39111872", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Datasets that involving arsenic-treated rice root and the “study type” that was restricted to “Expression profiling by array” were selected and downloaded from Gene Expression Omnibus (GEO) database."}, {"asset": "source:pmid:39111872", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed genes (DEGs) between the arsenic-treated group and the control group were obtained using the online web tool GEO2R."}, {"asset": "source:pmid:39111872", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Eighty common DEGs from the two datasets, including sixty-three up-regulated and seventeen down-regulated genes, were then selected."}, {"asset": "source:pmid:39111872", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Finally, five genes [Os01g0644000, PRDX6 (Os07g0638400), PRX112 (Os07g0677300), ENO1(Os06g0136600), LOGL9 (Os09g0547500)] were verified and could serve as the best candidates associated with rice root in response to arsenic stress."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using GEO2R on the GEO expression profiles GSE25206 and GSE71492, the study identified 80 common differentially expressed genes and nominated five hub genes associated with rice-root responses to arsenic stress.", "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:39111872"], "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:GSE25206"], "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:GSE25206"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39111872", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1265/ehpm.24-00095", "sha256": "sha256:7c7f5dbaf607dd0c69841a432f323a01bc15acf06196ed0a672464e0300dd049", "bytes": 28875, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1265/ehpm.24-00095", "version": null, "note": "Full article fetched from PMC; 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