Identification of latent biomarkers in connection with progression and prognosis in oral cancer by comprehensive bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34384424", "kind": "science-record", "revision": 8, "content_hash": "sha256:c14e0337cc78f0c8c076ad1e1e84a9050d923ea050790acfb7da8a74900b3210", "created_at": "2026-11-01T15:41:47Z", "updated_at": "2026-11-01T22:47:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of latent biomarkers in connection with progression and prognosis in oral cancer by comprehensive bioinformatics analysis.", "doi": "10.1186/s12957-021-02360-w", "pmid": "34384424", "authors": ["Abdusemer Reyimu", "Ying Chen", "Xudong Song", "Wubi Zhou", "Jingjing Dai", "Feng Jiang"], "journal": "World journal of surgical oncology", "year": 2021, "abstract": "BACKGROUND: Oral cancer (OC) is a common and dangerous malignant tumor with a low survival rate. However, the micro level mechanism has not been explained in detail.\nMETHODS: Gene and miRNA expression micro array data were extracted from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) and miRNAs (DE miRNAs) were identified by R software. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of genes and genomes (KEGG) pathway analysis were used to assess the potential molecular mechanisms of DEGs. Cytoscape software was utilized to construct protein-protein interaction (PPI) network and miRNA-gene network. Central genes were screened out with the participation of gene degree, molecular complex detection (MCODE) plugin, and miRNA-gene network. Then, the identified genes were checked by The Cancer Genome Atlas (TCGA) gene expression profile, Kaplan-Meier data, Oncomine, and the Human Protein Atlas database. Receiver operating characteristic (ROC) curve was drawn to predict the diagnostic efficiency of crucial gene level in normal and tumor tissues. Univariate and multivariate Cox regression were used to analyze the effect of dominant genes and clinical characteristics on the overall survival rate of OC patients.\nRESULTS: Gene expression data of gene expression profiling chip(GSE9844, GSE30784, and GSE74530) were obtained from GEO database, including 199 tumor and 63 non-tumor samples. We identified 298 gene mutations, including 200 upregulated and 98 downregulated genes. GO functional annotation analysis showed that DEGs were enriched in extracellular structure and extracellular matrix containing collagen. In addition, KEGG pathway enrichment analysis demonstrated that the DEGs were significantly enriched in IL-17 signaling pathway and PI3K-Akt signaling pathway. Then, we detected three most relevant modules in PPI network. Central genes (CXCL8, DDX60, EIF2AK2, GBP1, IFI44, IFI44L, IFIT1, IL6, MMP9,CXCL1, CCL20, RSAD2, and RTP4) were screened out with the participation of MCODE plugin, gene degree, and miRNA-gene network. TCGA gene expression profile and Kaplan-Meier analysis showed that high expression of CXCL8, DDX60, IL6, and RTP4 was associated with poor prognosis in OC patients, while patients with high expression of IFI44L and RSAD2 had a better prognosis. The elevated expression of CXCL8, DDX60, IFI44L, RSAD2, and RTP44 in OC was verified by using Oncomine database. ROC curve showed that the mRNA levels of these five genes had a helpful diagnostic effect on tumor tissue. The Human Protein Atlas database showed that the protein expressions of DDX60, IFI44L, RSAD2, and RTP44 in tumor tissues were higher than those in normal tissues. Finally, univariate and multivariate Cox regression showed that DDX60, IFI44L, RSAD2, and RTP44 were independent prognostic indicators of OC.\nCONCLUSION: This study revealed the potential biomarkers and relevant pathways of OC from publicly available GEO database, and provided a theoretical basis for elucidating the diagnosis, treatment, and prognosis of OC.", "claims": [{"id": "claim-method", "statement": "The R package of “limma” was used for analysis, and screening conditions were adjusted P < 0.05, |log2FC| > 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34384424", "locator": "sections[10] \"Identification of DEGs in OC\" paragraph 2", "quote": "The R package of “limma” was used for analysis, and screening conditions were adjusted P < 0.05, |log2FC| > 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusion of this article are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34384424", "locator": "sections[22] \"notes\" paragraph 1", "quote": "The datasets supporting the conclusion of this article are included within the article."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34384424"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34384424", "data:geo:GSE124566", "asset:table:pmid:34384424:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE124566"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:32Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 22301, "completion_tokens": 1301, "cached_tokens": 776}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:34384424", "type": "paper", "label": "pmid:34384424"}, {"id": "source:pmid:34384424", "type": "manuscript", "label": "PMID 34384424 full text"}, {"id": "data:geo:GSE124566", "type": "dataset", "label": "GEO GSE124566"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34384424", "type": "paper", "label": "pmid:34384424"}, {"id": "source:pmid:34384424", "type": "manuscript", "label": "PMID 34384424 full text"}, {"id": "data:geo:GSE124566", "type": "dataset", "label": "GEO GSE124566"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34384424", "type": "extraction", "used": ["source:pmid:34384424"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE124566", "type": "accession_resolution", "used": ["data:geo:GSE124566"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:34384424", "parent_hash": "sha256:38e6b77567ca37f2cf894bee7cbf7b964b38b7b95396b4c7f926aa427b5d5e0b", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE124566 licence not read", "asset:data:geo:GSE124566 not downloaded", "asset:data:geo:GSE30784 licence not read", "asset:data:geo:GSE30784 not downloaded", "asset:data:geo:GSE74530 licence not read", "asset:data:geo:GSE74530 not downloaded", "asset:data:geo:GSE9844 licence not read", "asset:data:geo:GSE9844 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The R package of “limma” was used for analysis, and screening conditions were adjusted P < 0.05, |log2FC| > 1."], "order_basis": "analysis_only", "id": "assay:1"}]}