Identification of key miRNAs and their targets in peripheral blood mononuclear cells of IgA nephropathy using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34190177", "kind": "science-record", "revision": 5, "content_hash": "sha256:019cb908e4209bfaa9b82015efe1036bd43ba972804e4dd1bbb8375d0c5f1517", "created_at": "2026-11-01T15:41:40Z", "updated_at": "2026-11-01T22:04:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of key miRNAs and their targets in peripheral blood mononuclear cells of IgA nephropathy using bioinformatics analysis.", "doi": "10.1097/MD.0000000000026495", "pmid": "34190177", "authors": ["Ling Liu", "YaZhen Yang", "Dongrong Yu"], "journal": "Medicine", "year": 2021, "abstract": "BACKGROUND: Currently, renal biopsy is the gold standard for clinical diagnosis and evaluation the degrees of IgA nephropathy. However, renal biopsy is an invasive examination and not suitable for long-term follow-up IgA nephropathy. The activation of peripheral blood mononuclear cells (PBMCs) are related to IgA nephropathy, but the key molecular marker and target of PBMCs for evaluating the progression and prognosis of IgA nephropathy is still unclear.\nMETHODS: We downloaded gene expression omnibus series 25590 (GSE25590) datasets, of which PBMCs from IgA nephrology (IgAN) and healthy patients, from the gene expression omnibus (GEO) database. Differentially expressed miRNAs (DEMs) between IgAN and healthy patients were identified. The Funrich software was used to predict the differentially expressed genes (DEGs). Gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyzes of overlapping genes were analyzed at the function level on DAVID 6.8. We used search Tool for the retrieval of interacting genes (STRING) online database constructed the protein-protein interaction (PPI) network. Then we further analyzed the hub genes by Cytoscape software and the hub miRNA by TargetScan.\nRESULTS: We identified 418 DEMs from the GSE25590 datasets. The upstream transcription factors SP1 regulates most DEMs. According to the GO and KEGG results, the DEGs were enriched in the MAPK signaling pathway and small GTPase mediated signal transduction. SYN1, SYT4, RBFOX1, KCNC1, VAMP2, FBXO11, ASB9, SYT9, KLHL5, and KRAS were identified as hub genes. Hsa-miR-532-5p, hsa-miR-92a, hsa-miR-328, hsa-miR-137, hsa-miR-153, hsa-miR-9-5p, hsa-miR-140-5p, hsa-miR-217, hsa-miR-155, and hsa-miR-212 were predicted as hub miRNAs.\nCONCLUSIONS: The DEMs and DEGs re-analysis provided potential key genes and hub miRNA of PMBCs, which may help to monitor the happening and prognosis of IgAN.", "claims": [{"id": "claim-data-access", "statement": "Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34190177", "locator": "sections[15] \"Footnotes\" paragraph 2", "quote": "Data sharing not applicable to this article as no datasets were generated or analyzed during the current study."}], "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:34190177"], "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:GSE25590"], "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:GSE25590"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34190177", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000026495", "sha256": 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{"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM627751", "GSM627779", "GSM627781", "GSM627926", "GSM627964", "GSM627983", "GSM627984", "GSM627998", "GSM627999", "GSM628000", "GSM628001", "GSM628002", "GSM628003", "GSM628004"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "7731", "taxon": "Homo sapiens", "title": "miR-148b modulates the C1GALT1 expression explaining the abnormal glycosylation process in IgA Nephropathy", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:34190177:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:8eb0bca914ced95c06e0fa9057bc0361fe5c136fd4ec4866689d08620c4257e1", "bytes": 478, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "Top 10 targeted genes predicted by up- regulated and down-regulated DEMs.", "structure": {"pmcid": "PMC8257889", "section_index": 10, "section_title": "Prediction upstream transcription factors and downstream target genes of differentially expressed miRNAs", "row_count": 11, "column_count": 2}, "table": {"label": "Table 1", "caption": "Top 10 targeted genes predicted by up- regulated and down-regulated DEMs.", "rows": [["Predicted by up-regulated DEMs", "Predicted by down-regulated DEMs"], ["CDC42EP3", "PCNP"], ["PFN2", "KCNT2"], ["IGIP", "KRTAP19–6"], ["SHISA7", "MSR1"], ["RASL11B", "NAT8L"], ["BTC", "ERBB4"], ["MRPL34", "NUP107"], ["GSG1L", "NOA1"], ["RGN", "CCDC126"], ["GAD1", "ELOVL5"]], "row_count": 11, "column_count": 2, "numeric_cells": 6, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:34190177:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:21be3a5699df8bd1d34ae3329c2830b4081d517cb5f3b5935b9a4b00c535f09e", "bytes": 651, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#T2", "version": null, "note": "A summary of miRNAs that regulate hub genes.", "structure": {"pmcid": "PMC8257889", "section_index": 12, "section_title": "Protein–protein interaction network construction and searching for hub genes", "row_count": 6, "column_count": 6}, "table": {"label": "Table 2", "caption": "A summary of miRNAs that regulate hub genes.", "rows": [["", "Gene", "Predicted miRNA", "", "Gene", "Predicted miRNA"], ["1", "KRAS", "hsa-miR-532-5p hsa-miR-142-3p hsa-miR-155", "2", "RBFOX1", "hsa-miR-92a hsa-miR-92b hsa-miR-25"], ["3", "VAMP2", "hsa-miR-328 hsa-miR-185 hsa-miR-520a-3p", "4", "KCNC1", "hsa-miR-137 hsa-let-7b hsa-let-7a"], ["5", "SYN1", "hsa-miR-153", "6", "SYN4", "hsa-miR-9-5p"], ["7", "KLHL5", "hsa-miR-140-5p", "8", "ASB9", "hsa-miR-217"], ["9", "FBXO11", "hsa-miR-155", "10", "SYT9", "hsa-miR-212 hsa-miR-133a hsa-miR-133b"]], "row_count": 6, "column_count": 6, "numeric_cells": 21, "header_rows": 1, "locator": "section[12]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE25590 not downloaded", "asset:data:geo:GSE25590 licence not read"]}, "analysis": {"state": "complete", "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": "protein-protein interaction"}}], "targets": [], "gaps": []}, "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE25590"], "resolved_accessions": ["GSE25590"], "statements": ["Data sharing not applicable to this article as no datasets were generated or analyzed during the current study."], "basis": "The paper names GSE25590 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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