Identification and validation of novel biomarker TRIM8 related to cervical cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36353542", "kind": "science-record", "revision": 4, "content_hash": "sha256:a36e78a808e1bf2988e62eeb6ab1188d4d6785e7c317149da951caf21ab3d69f", "created_at": "2026-11-01T18:15:48Z", "updated_at": "2026-11-01T22:08:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of novel biomarker TRIM8 related to cervical cancer.", "doi": "10.3389/fonc.2022.1002040", "pmid": "36353542", "authors": ["Li Zhang", "Youli Dan", "Chaoyang Ou", "Hongyan Qian", "Yi Yin", "Min Tang", "Qian He", "Chen Peng", "Aiqin He"], "journal": "Frontiers in oncology", "year": 2022, "abstract": "Background: Cervical cancer, as a common gynecological disease, endangers female health. Give the lack of effective biomarkers for the diagnosis and treatment of cervical cancer, this paper aims to analyze the Gene Expression Omnibus (GEO) data sets using comprehensive bioinformatics tools, and to identify biomarkers associated with the cancer in patient samples.\nMethods: The bioinformatics methods were used to extract genes related to cervical cancer from GSE39001, while the GEO2R online tool to elaborate on differentially expressed genes (DEGs) in normal and cancer samples, and to clarify related genes and functions. The results were verified by IHC, WB, CCK-8, clone formation and flow cytometry experiments.\nResults: A total of 2,859 DEGs were identified in the GEO microarray dataset. We extracted genes associated with both ubiquitination and autophagy from the key modules of weighted gene co-expression network analysis (WGCNA), and the analysis showed that TRIM8 was of great significance for the diagnosis and prognosis of cervical cancer. Besides, experimental validation showed the high TRIM8 expression in cervical cancer, as well as its involvement in the proliferation of cervical cancer cells.\nConclusion: We identified a biomarker (TRIM8) that may be related to cervical cancer through a series of analyses on the GEO dataset. Experimental verification confirmed the inhibition of cervical cancer cells proliferation by lowering TRIM8 expression. Therefore, TRIM8 can be adopted as a new biomarker of cervical cancer to develop new therapeutic targets.", "claims": [{"id": "claim-method", "statement": "We utilized GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE39001) online website to analyze all genes of normal and cancer samples, and downloaded corresponding files to screen DEGs. The DEGs were selected based on the adjustment p value <0.05 and | log fold change (FC) | >0.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36353542", "locator": "sections[4] \"Identification of DEGs and functional enrichment analysis\" paragraph 2", "quote": "We utilized GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE39001) online website to analyze all genes of normal and cancer samples, and downloaded corresponding files to screen DEGs. The DEGs were selected based on the adjustment p value <0.05 and | log fold change (FC) | >0.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE39001.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36353542", "locator": "sections[34] \"Data availability statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE39001."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified a biomarker (TRIM8) that may be related to cervical cancer through a series of analyses on the GEO dataset.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36353542", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We identified a biomarker (TRIM8) that may be related to cervical cancer through a series of analyses on the GEO dataset."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified a biomarker (TRIM8) that may be related to cervical cancer through a series of analyses on the GEO dataset.", "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:36353542"], "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:GSE39001"], "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:GSE39001"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36353542", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2022.1002040", "sha256": "sha256:7c12bfa3a1b1d63af4d6e138dded2421e3b93c621b5b05e1807d848a3af348d1", "bytes": 48484, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2022.1002040", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9638460", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE39001", "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=GSE39001", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39001", "version": null, "note": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE39001.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Publicly available datasets were analyzed in this study. 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"GSM953556", "GSM953557", "GSM953558", "GSM953559", "GSM953560", "GSM953561", "GSM953562", "GSM953563", "GSM953564", "GSM953565", "GSM953566", "GSM953567", "GSM953568", "GSM953569", "GSM953570"], "sample_count": 79, "group_sizes": null, "group_sizes_basis": null, "platform": "201;6244", "taxon": "Homo sapiens", "title": "Mitosis is the main pathway altered in cervical cancer and is a source of potential markers for screening and survival, and therapeutic targets.", "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:GSE39001 not downloaded", "asset:data:geo:GSE39001 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, 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The DEGs were selected based on the adjustment p value <0.05 and | log fold change (FC) | >0.5."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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The results were verified by IHC, WB, CCK-8, clone formation and flow cytomet"], "order_basis": "paper_text_order:695", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["tions. The results were verified by IHC, WB, CCK-8, clone formation and flow cytometry experime"], "order_basis": "paper_text_order:703", "id": "assay:2"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ified by IHC, WB, CCK-8, clone formation and flow cytometry experiments. Results: A total of 2,859 DEGs"], "order_basis": "paper_text_order:730", "id": "assay:3"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tal of 2,859 DEGs were identified in the GEO microarray dataset. We extracted genes associated with", "t. Patients The paraffin specimens of tissue microarray used are provided by Nantong Tumor Hospital."], "order_basis": "paper_text_order:816", "id": "assay:4"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on Declaration of Helsinki. Cell culture and transfection The two human cervical cancer cell lines HeL", "ering RNA (siRNA) was used as the vector for transfection, and the instructions of siRNA kit were refe", "instructions of siRNA kit were referred for transfection. When the fusion degree of HeLa and SiHa cel", "% CO2. In this study, small interfering RNA (siRNA) was used as the vector for transfection, an"], "order_basis": "paper_text_order:3308", "id": "assay:5"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["Chinese Academy of Sciences. The cells were cultured in DMEM (HyClone, USA) medium containing 10% fe", "ion The two human cervical cancer cell lines HeLa and SiHa involved in this study were purchas", "for transfection. When the fusion degree of HeLa and SiHa cells reached 70%-80% and they were"], "order_basis": "paper_text_order:3362", "id": "assay:6"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Kaplan Meier"], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}