Identification and Validation of Key miRNAs for Colon Cancer Based on miRNA-Gene Integration Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38077476", "kind": "science-record", "revision": 5, "content_hash": "sha256:e4ac8811607845d2eeb8ddc9362dfc851311c13f0705ca828025bb1ddad2c2c9", "created_at": "2026-11-01T19:03:01Z", "updated_at": "2026-11-01T22:53:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Validation of Key miRNAs for Colon Cancer Based on miRNA-Gene Integration Analysis.", "doi": "10.2147/IJGM.S440340", "pmid": "38077476", "authors": ["Yi Ji", "Jialin Gu", "Hongqun Zhang", "Houxi Xu"], "journal": "International journal of general medicine", "year": 2023, "abstract": "Background: MicroRNAs (miRNAs) plays an essential role in the pathogenesis of colon cancer. This study aims to identify and verify key miRNAs that may serve as potential biomarkers for early diagnosis and treatment of colon cancer.\nMethods: Two miRNA microarray datasets (GSE53339 and GSE126093) were downloaded from the Gene Expression Omnibus (GEO) database, and the common differentially expressed miRNAs (DEMis) of both were identified by the \"limma\" package and the intersect function in R. Then, the miRwalk online tool was used to predict the target genes of the common DEMis and perform Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis on those DEMis. The miRNA-gene network was constructed using Cytoscape software to identify key miRNAs and validated using quantitative real-time PCR (qRT-PCR) and The Cancer Genome Atlas (TCGA) dataset information for experimental and external database validation, respectively. In addition, we explored the correlation between key miRNAs and infiltrating immune cells and immunotherapy biomarkers.\nResults: Fourteen common DEMis were identified from the GEO database, and five targeted genes were predicted. A microRNA-gene network was subsequently constructed to identify three key miRNAs (miR-363-3p, miR-520e, and miR-330-5p). Both qRT-PCR and external database validation confirmed our findings. In addition, we found that miR-520e was significantly associated with infiltrating immune cells and established immune checkpoints.\nConclusion: Our study identified three key miRNAs that influence the development of colon cancer. In addition, further studies suggest that infiltrating immune cells may play an essential role in the pathogenesis of colon cancer. These findings assist in early diagnosis and precision-targeted therapies.", "claims": [{"id": "claim-method", "statement": "The GSE53339 and GSE126093 microarray datasets were analyzed using the “limma” R package (log|fold change| > 2, P-value < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38077476", "locator": "sections[4] \"Screening for Common Differentially Expressed miRNAs (DEMis)\" paragraph 2", "quote": "The GSE53339 and GSE126093 microarray datasets were analyzed using the “limma” R package (log|fold change| > 2, P-value < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated and/or analyzed during the current study are available in the GEO database repository: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53339 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126093.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38077476", "locator": "sections[24] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets generated and/or analyzed during the current study are available in the GEO database repository: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53339 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126093."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified three key miRNAs—miR-363-3p, miR-520e, and miR-330-5p—through analysis of two GEO miRNA microarray datasets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38077476", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Fourteen common DEMis were identified from the GEO database, and five targeted genes were predicted. A microRNA-gene network was subsequently constructed to identify three key miRNAs (miR-363-3p, miR-520e, and miR-330-5p)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified three key miRNAs—miR-363-3p, miR-520e, and miR-330-5p—through analysis of two GEO miRNA microarray datasets.", "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:38077476"], "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:GSE126093"], "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": {"fold_change": "imma R package with log|fold change| > 2 and P-value < 0"}, "inputs": ["data:geo:GSE126093"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38077476", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S440340", "sha256": "sha256:819c9d16c119dc681e24cef5c3044e3d52a156fe14a7fb64513256eee03c88cd", "bytes": 46974, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/IJGM.S440340", "version": null, "note": "Full article fetched from PMC; 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Mus musculus; Rattus norvegicus", "title": "Hsa_circ_101555 functions as a competing endogenous RNA of miR-597-5p to promote colorectal cancer progression [microRNA]", "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:GSE53339", "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=GSE53339", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE53339", "version": null, "note": "The datasets generated and/or analyzed during the current study are available in the GEO database repository: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53339 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126093.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated and/or analyzed during the current study are available in the GEO database repository: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53339 and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126093.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1289457", "GSM1289458", "GSM1289459", "GSM1289460", "GSM1289461", "GSM1289462", "GSM1289463", "GSM1289464", "GSM1289465", "GSM1289466", "GSM1289467", "GSM1289468"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "18058", "taxon": "Rattus norvegicus; Homo sapiens; Mus musculus", "title": "Differentially expressed miRNAs in colon cancer tissues vs normal colon tissues", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE126093 not downloaded", "asset:data:geo:GSE126093 licence not read", "asset:data:geo:GSE53339 not downloaded", "asset:data:geo:GSE53339 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "imma R package with log|fold change| > 2 and P-value < 0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The GSE53339 and GSE126093 microarray datasets were analyzed using the “limma” R package (log|fold change| > 2, P-value < 0.05)."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "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": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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