Dysregulation of cell cycle related genes and microRNAs distinguish the low- from high-risk of prostate cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25257132", "kind": "science-record", "revision": 6, "content_hash": "sha256:23767a41d73b5ac1e97b0e40b7898dec36d203bb3c66657a418b57033166ae8b", "created_at": "2026-11-01T15:40:06Z", "updated_at": "2026-11-01T21:58:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Dysregulation of cell cycle related genes and microRNAs distinguish the low- from high-risk of prostate cancer.", "doi": "10.1186/s13000-014-0156-1", "pmid": "25257132", "authors": ["Jiling Wen", "Rongbing Li", "Xiaofei Wen", "Guangming Chou", "Jiasun Lu", "Xuelei Wang", "Yongchao Jin"], "journal": "Diagnostic pathology", "year": 2014, "abstract": "BACKGROUND: Prostate cancer (PCa) is a biologically heterogeneous disease with considerable variation in clinical aggressiveness. In this study, bioinformatics was used to detect the patterns of gene expression alterations of PCa patients.\nMETHODS: The gene expression profile GSE21034 and GSE21036 were downloaded from Gene Expression Omnibus (GEO) database. Significantly changed mRNA transcripts and microRNAs were identified between subtypes with favorable (cluster 2) and unfavorable (cluster 5) prognosis by two-side unequal variances t test. MicroRNAs and their potential target genes were identified by TargetScan and miRTarBase, respectively. Besides, the overlapped genes between the target genes of microRNAs and mRNA transcripts were assessed by Fisher' exact test (one side). The functional annotation was performed by DAVID, followed by construction of protein-protein interaction (PPI) network.\nRESULTS: Compared to cluster 2, 1556 up-regulated and 1288 down-regulated transcripts were identified in cluster 5. Total 28 microRNAs were up-regulated and 30 microRNAs were down-regulated in cluster 5. Besides, 12 microRNAs target transcripts were significantly overlapped with down-regulated transcripts in cluster 5 with none of them was found overlapped with up-regulated transcripts. Functional annotation showed that cell cycle was the most significant function. In the PPI network, BRCA1, CDK1, TK1 and TRAF2 were hub protein of signature genes in cluster 5, and TGFBR1, SMAD2 and SMAD4 were hub proteins of signature gnens in cluster 2.\nCONCLUSIONS: Our findings raise the possibility that genes related with cell cycle and dysregulated miRNA at diagnosis might have clinical utility in distinguishing low- from high-risk PCa patients.\nVIRTUAL SLIDES: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_156.", "claims": [{"id": "claim-method", "statement": "Two-side unequal variances t test was used to identify the differentially expressed mRNA transcripts between cluster 2 and cluster 5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25257132", "locator": "sections[4] \"Identification of differentially expressed mRNA transcripts and microRNAs\" paragraph 2", "quote": "Two-side unequal variances t test was used to identify the differentially expressed mRNA transcripts between cluster 2 and cluster 5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Normalized mRNA and microRNAs expression profile data (GSE21034 and GSE21036) were downloaded from Gene Expression Omnibus (GEO). MicroRNAs profiling data were available for 8 (classified as cluster 5) and 25 PCa patients (classified as cluster 2), while mRNA profiling data were available for 13 (classified as cluster 5) and 34 PCa patients (classified as cluster 2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25257132", "locator": "sections[3] \"Microarray datasets\" paragraph 2", "quote": "Normalized mRNA and microRNAs expression profile data (GSE21034 and GSE21036) were downloaded from Gene Expression Omnibus (GEO)."}, {"asset": "source:pmid:25257132", "locator": "sections[3] \"Microarray datasets\" paragraph 2", "quote": "MicroRNAs profiling data were available for 8 (classified as cluster 5) and 25 PCa patients (classified as cluster 2), while mRNA profiling data were available for 13 (classified as cluster 5) and 34 PCa patients (classified as cluster 2)."}], "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:25257132"], "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:GSE21034"], "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:GSE21034"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:25257132", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13000-014-0156-1", "sha256": "sha256:2377325675e804d79c8bde55735409ebf397a2cc12214863a4229f1b5550b18e", "bytes": 19280, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13000-014-0156-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4215008", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21034", "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=GSE21034", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21034", "version": null, "note": "Normalized mRNA and microRNAs expression profile data (GSE21034 and GSE21036) were downloaded from Gene Expression Omnibus (GEO). MicroRNAs profiling data were available for 8 (classified as cluster 5) and 25 PCa patients (classified as cluster 2), while mRNA profiling data were available for 13 (classified as cluster 5) and 34 PCa patients (classified as cluster 2).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Normalized mRNA and microRNAs expression profile data (GSE21034 and GSE21036) were downloaded from Gene Expression Omnibus (GEO). 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"MicroRNAs that significantly changed in cluster 2 and 5", "structure": {"pmcid": "PMC4215008", "section_index": 9, "section_title": "Identification of dysregulated microRNAs and their potential target gene", "row_count": 62, "column_count": 5}, "table": {"label": "Table 1", "caption": "MicroRNAs that significantly changed in cluster 2 and 5", "rows": [["", "MicroRNAs", "Fold-change", "P-value", "Chromosome region"], ["Up-regulated", "", "", "", ""], ["", "hsa-miR-151-3p", "1.08", "2.5 E-2", "8"], ["hsa-miR-1237", "1.33", "8.8 E-3", "11"], ["hsa-miR-548c-3p", "1.63", "2.6 E-2", "12"], ["hsa-miR-1228", "1.14", "1.8 E-2", "12"], ["hsa-miR-130b", "1.13", "9.2 E-3", "22"], ["hsa-miR-210", "1.17", "3.5 E-2", "11p15.5"], ["hsa-miR-141", "1.07", "1.18 E-2", "12p13.31"], ["hsa-miR-19b-1*", "1.30", "4.06 E-2", "13q31.3"], ["hsa-miR-627", "1.23", "2.65 E-2", "15q15.1"], ["hsa-miR-1225-3p", "1.15", "4.85 E-2", "16p13.3"], ["hsa-miR-33b", "2.10", "4.08 E-3", "17p11.2"], ["hsa-miR-423-3p", "1.22", 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"data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Two-side unequal variances t test was used to identify the differentially expressed mRNA transcripts between cluster 2 and cluster 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": ["build_graph", "centrality_scores", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE21034", "GSE21036"], "resolved_accessions": ["GSE21034", "GSE21036"], "statements": ["Normalized mRNA and microRNAs expression profile data (GSE21034 and GSE21036) were downloaded from Gene Expression Omnibus (GEO). MicroRNAs profiling data were available for 8 (classified as cluster 5) and 25 PCa patients (classified as cluster 2), while mRNA profiling data were available for 13 (classified as cluster 5) and 34 PCa patients (classified as cluster 2)."], "basis": "The paper names GSE21034, GSE21036 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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