Identification of Potential miRNA-mRNA Regulatory Network in the Development of Oral Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36033831", "kind": "science-record", "revision": 4, "content_hash": "sha256:d201bc58d52506147fbe8574d8ce4bc735d459b961979e200e26229338c99b45", "created_at": "2026-11-01T18:15:12Z", "updated_at": "2026-11-01T22:07:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Potential miRNA-mRNA Regulatory Network in the Development of Oral Cancer.", "doi": "10.1155/2022/9376608", "pmid": "36033831", "authors": ["Yun Yang", "Xin Xin", "Ting Xu"], "journal": "Disease markers", "year": 2022, "abstract": "Background: Oral cancer is a difficult question in modern medical system, and there are few effective strategies to completely heal these diseases. This research investigated the miRNA-mRNA network in oral cancer development via bioinformatics excavation.\nMethods: GSE28100 and GSE23558 in the GEO database were selected for bioinformatics analysis. The datasets were analyzed with GEO2R to obtain the related matrix files. The hot plot and heatmap of the matrix files were drawn with R language. The MiRDIP database was applied to predict and screen the targets of miRNAs. The DEGs in the matrix files were analyzed with the DAVID database and visualized with R language for enrichment analysis. The PPI-network of the DEGs was established with the STRING database and Cytoscape. Besides, the miRNA-mRNA was visualized by Cytoscape.\nResults: 35 genes were identified as the DEGs in GES28100. 1651 genes were identified as the DEGs in GSE23558. 143 common genes in the targets of miRNAs in GSE28100 and the DEGs in GSE the targets of DEGs in GES28100 and common genes were enriched in the PI3K/AKT pathway, MAPK pathway, etc. The DEGs in GSE28100 and GSE23558 were involved in the regulations of transcription from RNA polymerase II promoter and DNA transcription. The DEGs in GSE28100 and GSE23558 were established with the miRNA-mRNA network.\nConclusion: This research identified miR-15b-5p, miR-199a-3p, miR-21-5p, miR-424-5p, and miR-454-3p as the biomarker of oral cancer and established the miRNA-mRNA network in oral progression.", "claims": [{"id": "claim-method", "statement": "The raw data of GSE28100 and GSE23558 were analyzed with GEO2R tool, and the related matrix files were normalized with the R language. The genes in GSE28100 and GSE23558 with |LogFC| ≥ 2 and P < 0.05 were selected as the DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36033831", "locator": "sections[4] \"2.2. Differential Expression Genes (DEGs)\" paragraph 2", "quote": "The raw data of GSE28100 and GSE23558 were analyzed with GEO2R tool, and the related matrix files were normalized with the R language. The genes in GSE28100 and GSE23558 with |LogFC| ≥ 2 and P < 0.05 were selected as the DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data to support the findings of this study is available on reasonable request from the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36033831", "locator": "sections[13] \"Data Availability\" paragraph 2", "quote": "Data to support the findings of this study is available on reasonable request from the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "35 genes were identified as the DEGs in GES28100.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36033831", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "35 genes were identified as the DEGs in GES28100."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "35 genes were identified as the DEGs in GES28100.", "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:36033831"], "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:GSE23558"], "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:GSE23558"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36033831", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/9376608", "sha256": "sha256:a166da94b32f94a4417a509543a52fce8aff95ab07e25a10986ddf83e02a23a5", "bytes": 19770, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/9376608", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9410825", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE23558", "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=GSE23558", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23558", "version": null, "note": "Data to support the findings of this study is available on reasonable request from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data to support the findings of this study is available on reasonable request from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM577914", "GSM577915", "GSM577916", "GSM577917", "GSM577918", "GSM577919", "GSM577920", "GSM577921", "GSM577922", "GSM577923", "GSM577924", "GSM577925", "GSM577926", "GSM577927", "GSM577928", "GSM577929", "GSM577930", "GSM577931", "GSM577932", "GSM577933", "GSM577934", "GSM577935", "GSM577936", "GSM577937", "GSM577938", "GSM577939", "GSM577940", "GSM577941", "GSM577942", "GSM577943", "GSM577944", "GSM577945"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Gene Expression Profiling of Oral Squamous Cell Carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE28100", "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=GSE28100", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28100", "version": null, "note": "Data to support the findings of this study is available on reasonable request from the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data to support the findings of this study is available on reasonable request from the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM696148", "GSM696149", "GSM696150", "GSM696151", "GSM696152", "GSM696153", "GSM696154", "GSM696155", "GSM696156", "GSM696157", "GSM696158", "GSM696159", "GSM696160", "GSM696161", "GSM696162", "GSM696163", "GSM696164", "GSM696165", "GSM696166", "GSM696167"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "10850", "taxon": "Homo sapiens", "title": "Differential expression of microRNAs between oral squamous cell carcinoma and healthy control tongues", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE23558 not downloaded", "asset:data:geo:GSE23558 licence not read", "asset:data:geo:GSE28100 not downloaded", "asset:data:geo:GSE28100 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R differential-expression analysis with DEGs selected by |LogFC| ≥ 2 and P < 0.05", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The raw data of GSE28100 and GSE23558 were analyzed with GEO2R tool, and the related matrix files were normalized with the R language. The genes in GSE28100 and GSE23558 with |LogFC| ≥ 2 and P < 0.05 were selected as the DEGs."}}], "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", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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