Reconstruction and analysis of circRNA‑miRNA‑mRNA network in the pathology of cervical cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30816541", "kind": "science-record", "revision": 8, "content_hash": "sha256:d19a713eb4652c3f60c17da60a610bcbe3bac2a753c9c0ae6cc91ec961557fcf", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:43:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Reconstruction and analysis of circRNA‑miRNA‑mRNA network in the pathology of cervical cancer.", "doi": "10.3892/or.2019.7028", "pmid": "30816541", "authors": ["Yuexiong Yi", "Yanyan Liu", "Wanrong Wu", "Kejia Wu", "Wei Zhang"], "journal": "Oncology reports", "year": 2019, "abstract": "The present study was performed with the aim of understanding the mechanisms of pathogenesis and providing novel biomarkers for cervical cancer by constructing a regulatory circular (circ)RNA‑micro (mi)RNA‑mRNA network. Using an adjusted P-value of <0.05 and an absolute log value of fold-change >1, 16 and 156 miRNAs from GSE30656 and The Cancer Genome Atlas (TCGA), 5,321 mRNAs from GSE63514, 4,076 mRNAs from cervical squamous cell carcinoma and endocervical adenocarcinoma (from TCGA) and 75 circRNAs from GSE102686 were obtained. Using RNAhybrid, Venn and UpSetR plot, 12 circRNA‑miRNA pairs and 266 miRNA‑mRNA pairs were obtained. Once these pairs were combined, a circRNA‑miRNA‑mRNA network with 11 circRNA nodes, 4 miRNA nodes, 153 mRNA nodes and 203 edges was constructed. By constructing the protein‑protein interaction network using Molecular Complex Detection scores >5 and >5 nodes, 7 hubgenes (RRM2, CEP55, CHEK1, KIF23, RACGAP1, ATAD2 and KIF11) were identified. By mapping the 7 hubgenes into the preliminary circRNA‑miRNA‑mRNA network, a circRNA‑miRNA‑hubgenes network consisting of 5 circRNAs (hsa_circRNA_000596, hsa_circRNA_104315, hsa_circRNA_400068, hsa_circRNA_101958 and hsa_circRNA_103519), 2 mRNAs (hsa‑miR‑15b and hsa‑miR‑106b) and 7 mRNAs (RRM2, CEP55, CHEK1, KIF23, RACGAP1, ATAD2 and KIF11) was constructed. There were 22 circRNA‑miRNA‑mRNA regulatory axes identified in the subnetwork. By analyzing the overall survival for the 7 hubgenes using the Gene Expression Profiling Interactive Analysis tool, higher expression of RRM2 was demonstrated to be associated with a significantly poorer overall survival. PharmGkb analysis identified single nucleotide polymorphisms (SNPs) of rs5030743 and rs1130609 of RRM2, which can be treated with cladribine and cytarabine. RRM2 was also indicated to be involved in the gemcitabine pathway. The 5 circRNAs (hsa_circRNA_000596, hsa_circRNA_104315, hsa_circRNA_400068, hsa_circRNA_101958 and hsa_circRNA_103519) may function as competing endogenous RNAs and serve critical roles in cervical cancer. In addition, cytarabine may produce similar effects to gemcitabine and may be an optional chemotherapeutic drug for treating cervical cancer by targeting rs5030743 and rs1130609 or other similar SNPs. However, the specific mechanism of action should be confirmed by further study.", "claims": [{"id": "claim-method", "statement": "The adjusted P-value (adj.p) and the absolute log value of fold-change (log|FC|) were calculated using R software with limma package (25).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30816541", "locator": "sections[5] \"Identification of differentially expressed (DE)-miRNAs, DE-circRNAs and DE-mRNAs\" paragraph 2", "quote": "The adjusted P-value (adj.p) and the absolute log value of fold-change (log|FC|) were calculated using R software with limma package (25)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30816541", "locator": "sections[28] \"Availability of data and materials\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published 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:30816541"], "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:30816541", "data:geo:GSE102686", "asset:table:pmid:30816541:1", "asset:table:pmid:30816541:2", "asset:table:pmid:30816541:3", "asset:table:pmid:30816541:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102686"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:14:03Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 46694, "completion_tokens": 1708, "cached_tokens": 784}}, "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:30816541", "type": "paper", "label": "pmid:30816541"}, {"id": "source:pmid:30816541", "type": "manuscript", "label": "PMID 30816541 full text"}, {"id": "data:geo:GSE102686", "type": "dataset", "label": "GEO GSE102686"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30816541", "type": "paper", "label": "pmid:30816541"}, {"id": "source:pmid:30816541", "type": "manuscript", "label": "PMID 30816541 full text"}, {"id": "data:geo:GSE102686", "type": "dataset", "label": "GEO GSE102686"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30816541", "type": "extraction", "used": ["source:pmid:30816541"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102686", "type": "accession_resolution", "used": ["data:geo:GSE102686"], "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:30816541", "parent_hash": "sha256:66721ff0e79e3e6017f35b5aa8c6094253ea3a6ea5ecbaca43de17f5cfa63d78", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE102686 licence not read", "asset:data:geo:GSE102686 not downloaded", "asset:data:geo:GSE30656 licence not read", "asset:data:geo:GSE30656 not downloaded", "asset:data:geo:GSE63514 licence not read", "asset:data:geo:GSE63514 not downloaded", "execution.not_run", "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 adjusted P-value (adj.p) and the absolute log value of fold-change (log|FC|) were calculated using R software with limma package (25)."], "order_basis": "analysis_only", "id": "assay:1"}]}