Integrative analysis of miRNA-mRNA network in idiopathic membranous nephropathy by bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34703677", "kind": "science-record", "revision": 5, "content_hash": "sha256:791e36f3dc973709ac804205fd4f8916ed916319e1c136ccae0165921df87cbe", "created_at": "2026-11-01T17:36:22Z", "updated_at": "2026-11-01T22:47:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrative analysis of miRNA-mRNA network in idiopathic membranous nephropathy by bioinformatics analysis.", "doi": "10.7717/peerj.12271", "pmid": "34703677", "authors": ["Wenfang He", "Jinshi Zhang", "Shizhu Yuan", "Mingzhu Liang", "Weidong Chen", "Juan Jin"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: Currently, several specific antigens, M-type receptor for secretory phospholipase A2(PLA2R1), thrombospondin type-1 domain-containing 7A(THSD7A), and neural epidermal growth factor-like 1 protein (NELL-1), are discovered associated with the onset of idiopathic membranous nephropathy (IMN). But the pathomechanisms of IMN still need to be further claried. Understanding the mechanisms of IMN is required to improve its diagnosis and treatment.\nMETHODS: In this study, we constructed miRNA regulatory networks to investigate IMN development. Moreover, miRNAs and mRNAs that were differentially expressed between Idiopathic Membranous Nephropathy (IMN) patients and normal controls were examined using the GSE115857 dataset and our previous sequence study. DE miRNA target genes were determined based on the FUNRICH software, starBase, miRDB, and miRWalk, and an miRNA-mRNA network was designed using DE-mRNAs that were negatively correlated with DE-miRNAs. The miRNA-mRNA network contained 228 miRNA-mRNA pairs. Thereafter, we conducted KEGG pathway, GO functional annotation, immune-related gene screening, protein interaction networks, and potential hub gene analyses. Furthermore, 10 miRNAs and 10 genes were determined and preliminarily validated using the validation dataset from GEO. Finally, we identified which pair may offer more accurate diagnosis and therapeutic targets for IMN.\nRESULTS: Two miRNA-mRNA pairs, miR-155-5p-FOS and miR-146a-5p-BTG2, were differentially expressed in IMN, indicating that these genes may affect IMN through immune processes. These findings may offer more accurate diagnoses and therapeutic targets for IMN.", "claims": [{"id": "claim-method", "statement": "Differentially expressed mRNAs (DE-mRNAs) between IMN and non-IMN volunteer samples of GSE115857 were identified using the limma package in R (version 3.36.3) (Gentleman et al., 2004) with thresholds of —logFC—>1 and adjusted P-values <0.05. Differentially expressed miRNAs (DE-miRNAs) between the IMN and non-IMN volunteer samples were assessed using the EdgeR package (edgeR 3.14.0) (Robinson, McCarthy & Smyth, 2010) in R.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34703677", "locator": "sections[4] \"Acquisition of differential expression miRNAs and mRNAs\" paragraph 2", "quote": "Differentially expressed mRNAs (DE-mRNAs) between IMN and non-IMN volunteer samples of GSE115857 were identified using the limma package in R (version 3.36.3) (Gentleman et al., 2004) with thresholds of —logFC—>1 and adjusted P-values <0.05. Differentially expressed miRNAs (DE-miRNAs) between the IMN and non-IMN volunteer samples were assessed using the EdgeR package (edgeR 3.14.0) (Robinson, McCarthy & Smyth, 2010) in R."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The expression data is available at GEO: GSE115857, GSE133288, GSE64306.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34703677", "locator": "sections[20] \"Additional Information and Declarations\" paragraph 4", "quote": "The expression data is available at GEO: GSE115857, GSE133288, GSE64306."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Two miRNA-mRNA pairs, miR-155-5p-FOS and miR-146a-5p-BTG2, were differentially expressed in IMN, indicating that these genes may affect IMN through immune processes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34703677", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Two miRNA-mRNA pairs, miR-155-5p-FOS and miR-146a-5p-BTG2, were differentially expressed in IMN, indicating that these genes may affect IMN through immune processes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Two miRNA-mRNA pairs, miR-155-5p-FOS and miR-146a-5p-BTG2, were differentially expressed in IMN, indicating that these genes may affect IMN through immune processes.", "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:34703677"], "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:GSE115857"], "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:GSE115857"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34703677", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.12271", "sha256": "sha256:769eff1973dac5b564e7a33c73696c66639c03db64a32100d5f46a8fbdb06d76", "bytes": 22590, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.12271", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8487241", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE115857", "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=GSE115857", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE115857", "version": null, "note": "The expression data is available at GEO: GSE115857, GSE133288, GSE64306.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The expression data is available at GEO: GSE115857, GSE133288, GSE64306.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3191893", "GSM3191894", "GSM3191895", "GSM3191896", "GSM3191897", "GSM3191898", "GSM3191899", "GSM3191900", "GSM3191901", "GSM3191902", "GSM3191903", "GSM3191904", "GSM3191905", "GSM3191906", "GSM3191907", "GSM3191908", "GSM3191909", "GSM3191910", "GSM3191911", "GSM3191912", "GSM3191913", "GSM3191914", "GSM3191915", "GSM3191916", "GSM3191917", "GSM3191918", "GSM3191919", "GSM3191920", "GSM3191921", "GSM3191922", "GSM3191923", "GSM3191924", "GSM3191925", "GSM3191926", "GSM3191927", "GSM3191928", "GSM3191929", "GSM3191930", "GSM3191931", "GSM3191932", "GSM3191933", "GSM3191934", "GSM3191935", "GSM3191936", "GSM3191937", "GSM3191938", "GSM3191939", "GSM3191940", "GSM3191941", "GSM3191942", "GSM3191943", "GSM3191944", "GSM3191945", "GSM3191946", "GSM3191947", "GSM3191948", "GSM3191949", "GSM3191950", "GSM3191951", "GSM3191952", "GSM3191953", "GSM3191954", "GSM3191955", "GSM3191956", "GSM3191957", "GSM3191958", "GSM3191959", "GSM3191960", "GSM3191961", "GSM3191962", "GSM3191963", "GSM3191964", "GSM3191965", "GSM3191966", "GSM3191967", "GSM3191968", "GSM3191969", "GSM3191970", "GSM3191971", "GSM3191972", "GSM3191973", "GSM3191974", "GSM3191975", "GSM3191976", "GSM3191977", "GSM3191978"], "sample_count": 86, "group_sizes": null, "group_sizes_basis": null, "platform": "14951", "taxon": "Homo sapiens", "title": "SPECIFIC BIOMARKERS ASSOCIATED WITH CHRONIC RENAL LESIONS IN IGA NEPHROPATHY PATIENTS. 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