Integrated analysis and identification of nine-gene signature associated to oral squamous cell carcinoma pathogenesis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33928003", "kind": "science-record", "revision": 4, "content_hash": "sha256:c18cf00952776dcd5d5d4d4c95461462d171803834fff70237b8b885b0ea0fc0", "created_at": "2026-11-01T17:35:13Z", "updated_at": "2026-11-01T22:03:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated analysis and identification of nine-gene signature associated to oral squamous cell carcinoma pathogenesis.", "doi": "10.1007/s13205-021-02737-4", "pmid": "33928003", "authors": ["Monika Yadav", "Dibyabhaba Pradhan", "Rana P Singh"], "journal": "3 Biotech", "year": 2021, "abstract": "Oral squamous cell carcinoma (OSCC) is one of the leading cancers with poor disease survival rate. Herein, we explored molecular basis, in silico identification and in vitro verification of genes associated with OSCC. Five gene expression series including, GSE30784, GSE13601, GSE9844, GSE23558 and GSE37991 were screened for differentially expressed genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were enriched by cluster Profiler. Further, protein-protein interaction network was analysed and hub genes were verified. A total of 6476 (up-regulated: 2848; down-regulated: 3628) DEGs were identified among OSCC patients and healthy controls. Gene Ontology analysis indicated DEGs enrichment in cellular motility, invasion and adhesion processes. KEGG analysis revealed enrichment of PI3K-Akt signalling, focal adhesion and regulation of actin cytoskeleton pathways. Subsequently, nine DEGs including APP, EHMT1, ACACB, PCNA, PLAU, FST, HMGA2, LAMC2 and SPP1 were correlated with TCGA expression data along with significant association towards patient's survival, recognized as hub genes. This dysregulated mRNA signature of genes was validated in two OSCC cell lines with an anti-cancer agent, fisetin. Fisetin inhibited the expression of APP, EHMT1, PCNA, PLAU, FST, HMGA2, LAMC2, SPP1 and upregulated the expression of ACACB gene which were associated with growth inhibition of both the OSCC cell lines. The regulatory effect of fisetin supported crucial role of nine hub genes identified in OSCC. This study signified that hub genes and pathways might influence the aggressiveness of OSCC. Thus, the proposed hub genes could be potential diagnostic biomarker and drug targets for OSCC.\nSUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-021-02737-4.", "claims": [{"id": "claim-data-access", "statement": "Five gene expression series including, GSE30784, GSE13601, GSE9844, GSE23558 and GSE37991 were screened for differentially expressed genes (DEGs).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33928003", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Five gene expression series including, GSE30784, GSE13601, GSE9844, GSE23558 and GSE37991 were screened for differentially expressed genes (DEGs)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 6476 DEGs were identified among OSCC patients and healthy controls, and nine DEGs were recognized as hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:33928003", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A total of 6476 (up-regulated: 2848; down-regulated: 3628) DEGs were identified among OSCC patients and healthy controls."}, {"asset": "source:pmid:33928003", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Subsequently, nine DEGs including APP, EHMT1, ACACB, PCNA, PLAU, FST, HMGA2, LAMC2 and SPP1 were correlated with TCGA expression data along with significant association towards patient’s survival, recognized as hub genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 6476 DEGs were identified among OSCC patients and healthy controls, and nine DEGs were recognized 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:33928003"], "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:GSE13601"], "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:GSE13601"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33928003", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s13205-021-02737-4", "sha256": 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:33928003", "data:geo:GSE13601"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE13601"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:01:45Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2044, "completion_tokens": 1260, "cached_tokens": 128}}, "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:33928003", "type": "paper", "label": "pmid:33928003"}, {"id": "source:pmid:33928003", "type": "manuscript", "label": "PMID 33928003 full text"}, {"id": "data:geo:GSE13601", "type": "dataset", "label": "GEO GSE13601"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33928003", "type": "paper", "label": "pmid:33928003"}, {"id": "source:pmid:33928003", "type": "manuscript", "label": "PMID 33928003 full text"}, {"id": "data:geo:GSE13601", "type": "dataset", "label": "GEO GSE13601"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33928003", "type": "extraction", "used": ["source:pmid:33928003"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE13601", "type": "accession_resolution", "used": ["data:geo:GSE13601"], "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:33928003", "parent_hash": "sha256:2da0a6e80d4544d2645bac5e8bd15abaf413f89abf48ea1a43b136d5d90a9422", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE13601 licence not read", "asset:data:geo:GSE13601 not downloaded", "asset:data:geo:GSE23558 licence not read", "asset:data:geo:GSE23558 not downloaded", "asset:data:geo:GSE30784 licence not read", "asset:data:geo:GSE30784 not downloaded", "asset:data:geo:GSE37991 licence not read", "asset:data:geo:GSE37991 not downloaded", "asset:data:geo:GSE9844 licence not read", "asset:data:geo:GSE9844 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}