Comprehensive and Integrated Analysis Identifies ZEB1 as a Key Novel Gene in Oral Squamous Cell Carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36034202", "kind": "science-record", "revision": 4, "content_hash": "sha256:3e8f01eefc13c043b11d606811d3a0e0ef8db705f5ab7fe5637c61cf7e390dc1", "created_at": "2026-11-01T18:15:12Z", "updated_at": "2026-11-01T22:07:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive and Integrated Analysis Identifies ZEB1 as a Key Novel Gene in Oral Squamous Cell Carcinoma.", "doi": "10.1155/2022/4486104", "pmid": "36034202", "authors": ["Jie Ma", "Yu Yao", "De-Tao Tao", "Jia-Yi Yin", "Liang Chen", "Yong Cui", "Ying Wang", "Cong-Lin Hu", "Ming-Xing Tian", "Qiong Wang"], "journal": "Contrast media & molecular imaging", "year": 2022, "abstract": "Oral squamous cell carcinoma (OSCC) is the most common head and neck cancer with a poor prognosis. Therefore, it is crucial to explore molecular prognostic biomarkers for OSCC. ZEB1 (also known as δEF1) is a member of the zinc finger E-box binding protein family of transcription factors involved in various biological processes, including tumorigenesis, progression, and metastasis. Recent evidence suggests that ZEB1 has a role in the tumorigenicity of oral epithelial cells, although its mode of action needs to be investigated further. To better understand the relationship between ZEB1 and OSCC, we transfected the ZEB1-overexpressing oral squamous cell lines SCC9 and SCC25 with lentivirus and then extracted RNA from the cells for gene expression analysis. Furthermore, the GSE30784 dataset was downloaded from the Gene Expression Omnibus (GEO) database to identify potential biomarkers of OSCC and to assess the potential mechanisms. The criteria for identification of their DEGs were |logFC| > 1 and P < 0.05. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses were also carried out. Integrating the data from the PPI network and survival analysis identified that ZEB1 might be an independent prognostic biomarker in OSCC. In conclusion, integrated bioinformatics and microarray analysis identified the critical gene ZEB1 linked to the overall survival (OS) of patients with OSCC. ZEB1 could be applied as a prognostic biomarker to forecast the survival of patients with OSCC and might indicate innovative therapeutic indicators for OSCC.", "claims": [{"id": "claim-method", "statement": "We assessed the impact of the expression levels of ZEB1 on the OS of patients with OSCC. Patients were divided into low- and high-expression groups according to the median ZEB1 expression. The accuracy of the Cox mark was evaluated by receiver operating characteristic (ROC) analysis using the R package. The prognostic values of the low- and high-expression groups were assessed using Kaplan–Meier (KM) curves in the survival R package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36034202", "locator": "sections[8] \"2.6. Survival Analysis and Cox Regression Analysis\" paragraph 2", "quote": "We assessed the impact of the expression levels of ZEB1 on the OS of patients with OSCC. Patients were divided into low- and high-expression groups according to the median ZEB1 expression. The accuracy of the Cox mark was evaluated by receiver operating characteristic (ROC) analysis using the R package. The prognostic values of the low- and high-expression groups were assessed using Kaplan–Meier (KM) curves in the survival R package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36034202", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Integrating the data from the PPI network and survival analysis identified that ZEB1 might be an independent prognostic biomarker in OSCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36034202", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Integrating the data from the PPI network and survival analysis identified that ZEB1 might be an independent prognostic biomarker in OSCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Integrating the data from the PPI network and survival analysis identified that ZEB1 might be an independent prognostic biomarker in OSCC.", "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:36034202"], "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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the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9381230", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30784", "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=GSE30784", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30784", "version": null, "note": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The simulation experiment data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM764749", "GSM764750", "GSM764751", "GSM764752", "GSM764753", "GSM764754", "GSM764755", "GSM764756", "GSM764757", "GSM764758", "GSM764759", "GSM764760", "GSM764761", "GSM764762", "GSM764763", "GSM764764", "GSM764765", "GSM764766", "GSM764767", "GSM764768", "GSM764769", "GSM764770", "GSM764771", "GSM764772", "GSM764773", "GSM764774", "GSM764775", "GSM764776", "GSM764777", "GSM764778", "GSM764779", "GSM764780", "GSM764781", "GSM764782", "GSM764783", "GSM764784", "GSM764785", "GSM764786", "GSM764787", "GSM764788", "GSM764789", "GSM764790", "GSM764791", "GSM764792", "GSM764793", "GSM764794", "GSM764795", "GSM764796", "GSM764797", "GSM764798", "GSM764799", "GSM764800", "GSM764801", "GSM764802", "GSM764803", "GSM764804", "GSM764805", "GSM764806", "GSM764807", "GSM764808", "GSM764809", "GSM764810", "GSM764811", "GSM764812", "GSM764813", "GSM764814", "GSM764815", "GSM764816", "GSM764817", "GSM764818", "GSM764819", "GSM764820", "GSM764821", "GSM764822", "GSM764823", "GSM764824", "GSM764825", "GSM764826", "GSM764827", "GSM764828", "GSM764829", "GSM764830", "GSM764831", "GSM764832", "GSM764833", "GSM764834", "GSM764835", "GSM764836", "GSM764837", "GSM764838", "GSM764839", "GSM764840", "GSM764841", "GSM764842", "GSM764843", "GSM764844", "GSM764845", "GSM764846", "GSM764847", "GSM764848", "GSM764849", "GSM764850", "GSM764851", "GSM764852", "GSM764853", "GSM764854", "GSM764855", "GSM764856", "GSM764857", "GSM764858", "GSM764859", "GSM764860", "GSM764861", "GSM764862", "GSM764863", "GSM764864", "GSM764865", "GSM764866", "GSM764867", "GSM764868", "GSM764869", "GSM764870", "GSM764871", "GSM764872", "GSM764873", "GSM764874", "GSM764875", "GSM764876", "GSM764877", "GSM764878", "GSM764879", "GSM764880", "GSM764881", "GSM764882", "GSM764883", "GSM764884", "GSM764885", "GSM764886", "GSM764887", "GSM764888", "GSM764889", "GSM764890", "GSM764891", "GSM764892", "GSM764893", "GSM764894", "GSM764895", "GSM764896", "GSM764897", "GSM764898", "GSM764899", "GSM764900", "GSM764901", "GSM764902", "GSM764903", "GSM764904", "GSM764905", "GSM764906", "GSM764907", "GSM764908", "GSM764909", "GSM764910", "GSM764911", "GSM764912", "GSM764913", "GSM764914", "GSM764915", "GSM764916", "GSM764917", "GSM764918", "GSM764919", "GSM764920", "GSM764921", "GSM764922", "GSM764923", "GSM764924", "GSM764925", "GSM764926", "GSM764927", "GSM764928", "GSM764929", "GSM764930", "GSM764931", "GSM764932", "GSM764933", "GSM764934", "GSM764935", "GSM764936", "GSM764937", "GSM764938", "GSM764939", "GSM764940", "GSM764941", "GSM764942", "GSM764943", "GSM764944", "GSM764945", "GSM764946", "GSM764947", "GSM764948", "GSM764949", "GSM764950", "GSM764951", "GSM764952", "GSM764953", "GSM764954", "GSM764955", "GSM764956", "GSM764957", "GSM764958", "GSM764959", "GSM764960", "GSM764961", "GSM764962", "GSM764963", "GSM764964", "GSM764965", "GSM764966", "GSM764967", "GSM764968", "GSM764969", "GSM764970", "GSM764971", "GSM764972", "GSM764973", "GSM764974", "GSM764975", "GSM764976", "GSM764977"], "sample_count": 229, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling of oral squamous cell carcinoma (OSCC)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE30784 not downloaded", "asset:data:geo:GSE30784 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We assessed the impact of the expression levels of ZEB1 on the OS of patients with OSCC. 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