Identification of a lncRNA/circRNA-miRNA-mRNA network in Nasopharyngeal Carcinoma by deep sequencing and bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38434987", "kind": "science-record", "revision": 3, "content_hash": "sha256:e9dc65f67974c85568bfe56b462a36bc54e6c9194c17bf83c9a02eb613f3ea81", "created_at": "2026-11-01T19:20:22Z", "updated_at": "2026-11-01T21:32:37Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a lncRNA/circRNA-miRNA-mRNA network in Nasopharyngeal Carcinoma by deep sequencing and bioinformatics analysis.", "doi": "10.7150/jca.91546", "pmid": "38434987", "authors": ["Shilei Liu", "Xiaoxiao Li", "Qingming Xie", "Sai Zhang", "Xujun Liang", "Shisheng Li", "Pengfei Zhang"], "journal": "Journal of Cancer", "year": 2024, "abstract": "Background: Accumulating evidence indicates that non-coding RNAs (ncRNA), including long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), can function as competitive endogenous RNAs (ceRNAs) by binding to microRNAs (miRNAs) and regulating host gene expression at the transcriptional or post-transcriptional level. Dysregulation in ceRNA network regulation has been implicated in the occurrence and development of cancer. However, the lncRNA/circRNA-miRNA-mRNA regulatory network is still lacking in nasopharyngeal carcinoma (NPC). Methods: Differentially expressed genes (DEGs) were obtained from our previous sequencing data and Gene Expression Omnibus (GEO). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) were used to explore the biological functions of these common DEGs. Through a series of bioinformatic analyses, the lncRNA/circRNA-miRNA-mRNA network was established. In additional, the external data GSE102349 was used to test the prognostic value of the hub mRNAs through the Kaplan-Meier method. Results: We successfully constructed a lncRNA/circRNA-miRNA-mRNA network in NPC, consisting of 16 lncRNAs, 6 miRNAs, 3 circRNAs and 10 mRNAs and found that three genes (TOP2A, ZWINT, TTK) were significantly associated with overall survival time (OS) in patients. Conclusion: The regulatory network revealed in this study may help comprehensively elucidate the ceRNA mechanisms driving NPC, and provide novel candidate biomarkers for evaluating the prognosis of NPC.", "claims": [{"id": "claim-method", "statement": "In additional, the external data GSE102349 was used to test the prognostic value of the hub mRNAs through the Kaplan-Meier method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38434987", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "In additional, the external data GSE102349 was used to test the prognostic value of the hub mRNAs through the Kaplan-Meier method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The information presented in this article can be accessed through the GEO database, which can be found at: https://www.ncbi.nlm.nih.gov/geo. We have uploaded the raw sequencing data to the GEO database with serial number GSE227541 (data are to be held confidential until Dec 31, 2023). You may view our study at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227541.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38434987", "locator": "sections[24] \"Data availability statement\" paragraph 2", "quote": "The information presented in this article can be accessed through the GEO database, which can be found at: https://www.ncbi.nlm.nih.gov/geo. We have uploaded the raw sequencing data to the GEO database with serial number GSE227541 (data are to be held confidential until Dec 31, 2023). You may view our study at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227541."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We successfully constructed a lncRNA/circRNA-miRNA-mRNA network in NPC, consisting of 16 lncRNAs, 6 miRNAs, 3 circRNAs and 10 mRNAs and found that three genes (TOP2A, ZWINT, TTK) were significantly associated with overall survival time (OS) in patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38434987", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We successfully constructed a lncRNA/circRNA-miRNA-mRNA network in NPC, consisting of 16 lncRNAs, 6 miRNAs, 3 circRNAs and 10 mRNAs and found that three genes (TOP2A, ZWINT, TTK) were significantly associated with overall survival time (OS) in patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We successfully constructed a lncRNA/circRNA-miRNA-mRNA network in NPC, consisting of 16 lncRNAs, 6 miRNAs, 3 circRNAs and 10 mRNAs and found that three genes (TOP2A, ZWINT, TTK) were significantly associated with overall survival time (OS) in patients.", "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:38434987"], "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:GSE102349"], "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:GSE102349"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38434987", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.91546", "sha256": "sha256:95a450e343cb2276c1fe20b5c76c27d64d3de35b4da5169490ec30fdf1090034", "bytes": 39002, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/jca.91546", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10905391", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE102349", "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=GSE102349", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102349", "version": null, "note": "The information presented in this article can be accessed through the GEO database, which can be found at: https://www.ncbi.nlm.nih.gov/geo. We have uploaded the raw sequencing data to the GEO database with serial number GSE227541 (data are to be held confidential until Dec 31, 2023). You may view our study at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227541.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The information presented in this article can be accessed through the GEO database, which can be found at: https://www.ncbi.nlm.nih.gov/geo. We have uploaded the raw sequencing data to the GEO database with serial number GSE227541 (data are to be held confidential until Dec 31, 2023). You may view our study at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227541.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2735202", "GSM2735203", "GSM2735204", "GSM2735205", "GSM2735206", "GSM2735207", "GSM2735208", "GSM2735209", "GSM2735210", "GSM2735211", "GSM2735212", "GSM2735213", "GSM2735214", "GSM2735215", "GSM2735216", "GSM2735217", "GSM2735218", "GSM2735219", "GSM2735220", "GSM2735221", "GSM2735222", "GSM2735223", "GSM2735224", "GSM2735225", "GSM2735226", "GSM2735227", "GSM2735228", "GSM2735229", "GSM2735230", "GSM2735231", "GSM2735232", "GSM2735233", "GSM2735234", "GSM2735235", "GSM2735236", "GSM2735237", "GSM2735238", "GSM2735239", "GSM2735240", "GSM2735241", "GSM2735242", "GSM2735243", "GSM2735244", "GSM2735245", "GSM2735246", "GSM2735247", "GSM2735248", "GSM2735249", "GSM2735250", "GSM2735251", "GSM2735252", "GSM2735253", "GSM2735254", "GSM2735255", "GSM2735256", "GSM2735257", "GSM2735258", "GSM2735259", "GSM2735260", "GSM2735261", "GSM2735262", "GSM2735263", "GSM2735264", "GSM2735265", "GSM2735266", "GSM2735267", "GSM2735268", "GSM2735269", "GSM2735270", "GSM2735271", "GSM2735272", "GSM2735273", "GSM2735274", "GSM2735275", "GSM2735276", "GSM2735277", "GSM2735278", "GSM2735279", "GSM2735280", "GSM2735281", "GSM2735282", "GSM2735283", "GSM2735284", "GSM2735285", "GSM2735286", "GSM2735287", "GSM2735288", "GSM2735289", "GSM2735290", "GSM2735291", "GSM2735292", "GSM2735293", "GSM2735294", "GSM2735295", "GSM2735296", "GSM2735297", "GSM2735298", "GSM2735299", "GSM2735300", "GSM2735301", "GSM2735302", "GSM2735303", "GSM2735304", "GSM2735305", "GSM2735306", "GSM2735307", "GSM2735308", "GSM2735309", "GSM2735310", "GSM2735311", "GSM2735312", "GSM2735313", "GSM2735314"], "sample_count": 113, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Genomic Analysis of Nasopharyngeal Carcinoma Reveals TME-based Subtypes", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE227541", "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=GSE227541", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE227541", "version": null, "note": "The information presented in this article can be accessed through the GEO database, which can be found at: https://www.ncbi.nlm.nih.gov/geo. We have uploaded the raw sequencing data to the GEO database with serial number GSE227541 (data are to be held confidential until Dec 31, 2023). You may view our study at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227541.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The information presented in this article can be accessed through the GEO database, which can be found at: https://www.ncbi.nlm.nih.gov/geo. We have uploaded the raw sequencing data to the GEO database with serial number GSE227541 (data are to be held confidential until Dec 31, 2023). You may view our study at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227541.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM7102457", "GSM7102458", "GSM7102459", "GSM7102460", "GSM7102461", "GSM7102462", "GSM7102463", "GSM7102464", "GSM7102465", "GSM7102466", "GSM7102467", "GSM7102468", "GSM7102469", "GSM7102470"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "Identification a lncRNA/circRNA-miRNA-mRNA ceRNA network in Nasopharyngeal Carcinoma by deep sequencing and bioinformatics analysis", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE61218", "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=GSE61218", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE61218", "version": null, "note": "The information presented in this article can be accessed through the GEO database, which can be found at: https://www.ncbi.nlm.nih.gov/geo. We have uploaded the raw sequencing data to the GEO database with serial number GSE227541 (data are to be held confidential until Dec 31, 2023). You may view our study at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227541.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The information presented in this article can be accessed through the GEO database, which can be found at: https://www.ncbi.nlm.nih.gov/geo. We have uploaded the raw sequencing data to the GEO database with serial number GSE227541 (data are to be held confidential until Dec 31, 2023). You may view our study at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227541.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1499764", "GSM1499765", "GSM1499766", "GSM1499767", "GSM1499768", "GSM1499769", "GSM1499770", "GSM1499771", "GSM1499772", "GSM1499773", "GSM1499774", "GSM1499775", "GSM1499776", "GSM1499777", "GSM1499778", "GSM1499779"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "19061", "taxon": "Homo sapiens", "title": "mRNA and lncRNA gene expression profile of nasopharyngeal carcinoma", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE102349 not downloaded", "asset:data:geo:GSE102349 licence not read", "asset:data:geo:GSE227541 not downloaded", "asset:data:geo:GSE227541 licence not read", "asset:data:geo:GSE61218 not downloaded", "asset:data:geo:GSE61218 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In additional, the external data GSE102349 was used to test the prognostic value of the hub mRNAs through the Kaplan-Meier method."}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}], "targets": [], "gaps": []}, "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE102349", "GSE61218", "GSE227541"], "resolved_accessions": ["GSE102349", "GSE61218", "GSE227541"], "statements": ["The information presented in this article can be accessed through the GEO database, which can be found at: https://www.ncbi.nlm.nih.gov/geo. We have uploaded the raw sequencing data to the GEO database with serial number GSE227541 (data are to be held confidential until Dec 31, 2023). You may view our study at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227541."], "basis": "The paper names GSE102349, GSE61218, GSE227541 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:38434987", "data:geo:GSE102349"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE102349"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:10:39Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12973, "completion_tokens": 1640, "cached_tokens": 256}}, "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:38434987", "type": "paper", "label": "pmid:38434987"}, {"id": "source:pmid:38434987", "type": "manuscript", "label": "PMID 38434987 full text"}, {"id": "data:geo:GSE102349", "type": "dataset", "label": "GEO GSE102349"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38434987", "type": "paper", "label": "pmid:38434987"}, {"id": "source:pmid:38434987", "type": "manuscript", "label": "PMID 38434987 full text"}, {"id": "data:geo:GSE102349", "type": "dataset", "label": "GEO GSE102349"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38434987", "type": "extraction", "used": ["source:pmid:38434987"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE102349", "type": "accession_resolution", "used": ["data:geo:GSE102349"], "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:38434987", "parent_hash": "sha256:295a3bcd5e0da8810aac61cecf862dcefe587a794a76e72b594d72fb088fa7fd", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE102349 licence not read", "asset:data:geo:GSE102349 not downloaded", "asset:data:geo:GSE227541 licence not read", "asset:data:geo:GSE227541 not downloaded", "asset:data:geo:GSE61218 licence not read", "asset:data:geo:GSE61218 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": 1.0, "evidence": ["In additional, the external data GSE102349 was used to test the prognostic value of the hub mRNAs through the Kaplan-Meier method."], "order_basis": "analysis_only", "id": "assay:1"}]}