The biomarkers of key miRNAs and gene targets associated with extranodal NK/T-cell lymphoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35071774", "kind": "science-record", "revision": 6, "content_hash": "sha256:00358ea1bbc1425b662acec99547eabdd6dc2f739fb5537fa8b6028ac1d6e14d", "created_at": "2026-11-01T17:36:48Z", "updated_at": "2026-11-01T22:48:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The biomarkers of key miRNAs and gene targets associated with extranodal NK/T-cell lymphoma.", "doi": "10.1515/med-2021-0409", "pmid": "35071774", "authors": ["Yin-Yin Peng", "Hong-Bin Zhang", "Xin Wang", "Qing Xiao", "Shu-Liang Guo"], "journal": "Open medicine (Warsaw, Poland)", "year": 2022, "abstract": "Gene expression profiling studies have shown the pathogenetic role of oncogenic pathways in extranodal natural killer/T-cell lymphoma (ENKL). In this study, we aimed to identify the microRNAs (miRNAs) playing potential roles in ENKL, and to evaluate the genes and biological pathways associated to them. Gene expression profiles of ENKL patients were acquired from the gene expression omnibus (GEO) database. Most differentially expressed (DE)-miRNAs were identified in ENKL patients using limma package. Gene targets of the DE-miRNAs were collected from online databases (miRDB, miRWalk, miRDIP, and TargetScan), and used in Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses on Database for annotation, visualization, and integrated discovery database, and then used in protein-protein interaction (PPI) analysis on STRING database. Hub genes of the PPI network were identified in cytoHubba, and were evaluated in Biological networks gene ontology. According to the series GSE31377 and GSE43958 from GEO database, four DE-miRNAs were screened out: hsa-miR-363-3p, hsa-miR-296-5p, hsa-miR-155-5p, and hsa-miR-221-3p. Totally 164 gene targets were collected from the online databases, and used in the GO and KEGG pathway analyses and PPI network analysis. Ten hub genes of the PPI network were identified: AURKA, TP53, CDK1, CDK2, CCNB1, PLK1, CUL1, ESR1, CDC20, and PIK3CA. Those hub genes, as well as their correlative pathways, may be of diagnostic or therapeutic potential for ENKL, but further clinical evidence is still expected.", "claims": [{"id": "claim-method", "statement": "The limma R package v3.12 was applied and served as the processor.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35071774", "locator": "sections[4] \"Identification of DE-miRNAs\" paragraph 2", "quote": "The limma R package v3.12 was applied and served as the processor."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Original data of this study are from public databases. The R script as well as its output could be provided upon request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35071774", "locator": "sections[19] \"fn-group\" paragraph 1", "quote": "Original data of this study are from public databases. The R script as well as its output could be provided upon request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study used limma in R to analyze ENKL miRNA-expression profiles from GEO series GSE31377 and GSE43958 and identified four common differentially expressed miRNAs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35071774", "locator": "sections[1] \"Introduction\" paragraph 5", "quote": "To that end, we acquired typical gene expression profiles of ENKL patients from the Gene Expression Omnibus (GEO) database, and identified four miRNAs that are most differentially expressed (DE) in those ENKL patients using limma package in R."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study used limma in R to analyze ENKL miRNA-expression profiles from GEO series GSE31377 and GSE43958 and identified four common differentially expressed miRNAs.", "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:35071774"], "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:GSE31377"], "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:GSE31377"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35071774", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1515/med-2021-0409", "sha256": "sha256:31ba4abd1bc0df2cb0514dcec51501bd16cd6234aaa277d95826efc70b4c2f8e", "bytes": 23004, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1515/med-2021-0409", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8729226", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE31377", "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=GSE31377", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31377", "version": null, "note": "Original data of this study are from public databases. The R script as well as its output could be provided upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Original data of this study are from public databases. 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