Identification of biomarkers and construction of a microRNA‑mRNA regulatory network for clear cell renal cell carcinoma using integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33434215", "kind": "science-record", "revision": 8, "content_hash": "sha256:4c82eeb0021a8fddc06013df349780f2831bd6da72c2f94710d26635e938e8aa", "created_at": "2026-11-01T15:41:22Z", "updated_at": "2026-11-01T22:45:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of biomarkers and construction of a microRNA‑mRNA regulatory network for clear cell renal cell carcinoma using integrated bioinformatics analysis.", "doi": "10.1371/journal.pone.0244394", "pmid": "33434215", "authors": ["Miaoru Han", "Haifeng Yan", "Kang Yang", "Boya Fan", "Panying Liu", "Hongtao Yang"], "journal": "PloS one", "year": 2021, "abstract": "With the recent research development, the importance of microRNAs (miRNAs) in renal clear cell carcinoma (CCRCC) has become widely known. The purpose of this study is to screen out the potential biomarkers of renal clear cell carcinoma (CCRCC) by microarray analysis. The miRNA chip (GSE16441) and mRNA chip (GSE66270) related to CCRCC were downloaded from the Gene Expression Omnibus (GEO) database. After data filtering and pretreating, R platform and a series of analysis tools (funrich3.1.3, string, Cytoscape_ 3.2.1, David, etc.) were used to analyze chip data and identify the specific and highly sensitive biomarkers. Finally, by constructing the miRNA -mRNA interaction network, it was determined that five miRNAs (hsa-mir-199a-5p, hsa-mir-199b-5p, hsa-mir-532-3p and hsa-mir-429) and two key genes (ETS1 and hapln1) are significantly related to the overall survival rate of patients.", "claims": [{"id": "claim-method", "statement": "In order to further verify the characteristics of DEGS in the network and its correlation strength with survival, Cox regression analysis, Kaplan-Meier curve and log-rank analysis were adopted to study more about the survival of DEGS in the network.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33434215", "locator": "sections[14] \"3.5 Survival analyses\" paragraph 2", "quote": "In order to further verify the characteristics of DEGS in the network and its correlation strength with survival, Cox regression analysis, Kaplan-Meier curve and log-rank analysis were adopted to study more about the survival of DEGS in the network."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The chip data analyzed in this study are available in the Supporting Information files. These data are all from GeneExpression Omnibus (GEO) database http://www.ncbi.nlm.nih.gov/geo/. GSE16441 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16441, and GSE66270 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66270.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33434215", "locator": "sections[18] \"Data Availability\" paragraph 2", "quote": "The chip data analyzed in this study are available in the Supporting Information files. These data are all from GeneExpression Omnibus (GEO) database http://www.ncbi.nlm.nih.gov/geo/. GSE16441 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE16441, and GSE66270 was downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE66270."}], "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:33434215"], "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:GSE16441"], "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:GSE16441"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33434215", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0244394", "sha256": "sha256:9e6fc675b2efae8c35b725adf485f5eee1c19046c96a94a8f9bac5f510836deb", "bytes": 36339, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0244394", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7802940", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16441", "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=GSE16441", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16441", "version": null, "note": "The chip data analyzed in this study are available in the Supporting Information files. 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:33434215", "data:geo:GSE16441", "asset:table:pmid:33434215:1", "asset:table:pmid:33434215:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16441"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:25Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 31100, "completion_tokens": 2536, "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:33434215", "type": "paper", "label": "pmid:33434215"}, {"id": "source:pmid:33434215", "type": "manuscript", "label": "PMID 33434215 full text"}, {"id": "data:geo:GSE16441", "type": "dataset", "label": "GEO GSE16441"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33434215", "type": "paper", "label": "pmid:33434215"}, {"id": "source:pmid:33434215", "type": "manuscript", "label": "PMID 33434215 full text"}, {"id": "data:geo:GSE16441", "type": "dataset", "label": "GEO GSE16441"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33434215", "type": "extraction", "used": ["source:pmid:33434215"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16441", "type": "accession_resolution", "used": ["data:geo:GSE16441"], "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:33434215", "parent_hash": "sha256:5268e813e720c24f4edab2199c52565713671f1f387d38490b6528d22d0bd0d8", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE16441 licence not read", "asset:data:geo:GSE16441 not downloaded", "asset:data:geo:GSE66270 licence not read", "asset:data:geo:GSE66270 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["ers of renal clear cell carcinoma (CCRCC) by microarray analysis. The miRNA chip (GSE16441) and mRNA", "rix file (s) and GPL8659 Agilent human miRNA microarray rel12.0 platform files. According to the cor", "trix file (s) and GPL570 [HG-U133]_ Plus_ 2] Affymetrix human genome U133 Plus 2.0 array platform fi"], "order_basis": "paper_text_order:364", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["In order to further verify the characteristics of DEGS in the network and its correlation strength with survival, Cox regression analysis, Kaplan-Meier curve and log-rank analysis were adopted to study more about the survival of DEGS in the network."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}