Gestational Diabetes Mellitus Regulatory Network Identifies hsa-miR-145-5p and hsa-miR-875-5p as Potential Biomarkers.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31497041", "kind": "science-record", "revision": 8, "content_hash": "sha256:2787ab26d176ab4524f4032e8b9259bd20d831291f57bcf28449b3f79b5677a1", "created_at": "2026-11-01T15:40:49Z", "updated_at": "2026-11-01T22:00:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gestational Diabetes Mellitus Regulatory Network Identifies hsa-miR-145-5p and hsa-miR-875-5p as Potential Biomarkers.", "doi": "10.5812/ijem.86640", "pmid": "31497041", "authors": ["Mona Zamanian Azodi", "Mostafa Rezaei-Tavirani", "Majid Rezaei-Tavirani", "Reza Mahmoud Robati"], "journal": "International journal of endocrinology and metabolism", "year": 2019, "abstract": "BACKGROUND: Gestational diabetes mellitus (GDM) is pregnancy-related diabetes with vital risks for both mother and the fetus. Molecular studies represent one of the popular approaches for investigating mechanisms associated with the disease nature. One of which is through interaction network analysis via Cytoscape V. 3.6.1.\nMETHODS: In this study, the microRNA (miRNA) expression array of GSE98043 from gene expression omnibus (GEO) database was retrieved and screened. We identified 12 differentially expressed (DE) miRNAs (P ≤ 0.05) and nine target hub-bottleneck genes (disease score > 1) for GDM based on miRNA-target interactions created via plugin ClueGO + Cluepedia + STRING.\nRESULTS: MiRNA-target information showed that the miRNAs are mostly up-regulated and hsa-miR-145-5p and hsa-miR-875-5p targets the most genes. Among target genes, IL6, GCG, APOB, and ALB have the highest associations with DE-miRNAs. Gene ontology analysis based on biological processes identification via ClueGO + CluePedia, in addition, showed that target hub-bottlenecks are mainly related to metabolism functions and any changes in this regulatory network could impose fundamental alterations in these processes.\nCONCLUSIONS: It can be concluded that via these introduced miRNAs and their targets, the molecular tests for diagnosis and treatment of GDM can be improved after applying validation approaches.", "claims": [{"id": "claim-method", "statement": "Human samples of healthy controls and gestational diabetes mellitus were compared in terms of expression profiling of differentially expressed (DE)miRNA via GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31497041", "locator": "sections[3] \"3. Methods\" paragraph 2", "quote": "Human samples of healthy controls and gestational diabetes mellitus were compared in terms of expression profiling of differentially expressed (DE)miRNA via GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The current bioinformatics study is based on plasma miRNA expression profiling of GDM available online in gene expression omnibus (GEO) (www.ncbi.nlm.nih.gov/geo/). The dataset was assigned with GEO series accession number of GSE98043, which was based on the platform of GPL21575 (Agilent-070156 Human_miRNA_V21.0_Microarray 046064) using SurePrint human miRNA microarray (11).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31497041", "locator": "sections[3] \"3. Methods\" paragraph 2", "quote": "The current bioinformatics study is based on plasma miRNA expression profiling of GDM available online in gene expression omnibus (GEO) (www.ncbi.nlm.nih.gov/geo/). The dataset was assigned with GEO series accession number of GSE98043, which was based on the platform of GPL21575 (Agilent-070156 Human_miRNA_V21.0_Microarray 046064) using SurePrint human miRNA microarray (11)."}], "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:31497041"], "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:GSE98043"], "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:GSE98043"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31497041", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.5812/ijem.86640", "sha256": "sha256:ee4b58e0df871f9fce94f0151fda5fd5c07cd54d576566f4fe2592420fc5e126", "bytes": 17071, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.5812/ijem.86640", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6678685", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE98043", "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=GSE98043", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE98043", "version": null, "note": "The current bioinformatics study is based on plasma miRNA expression profiling of GDM available online in gene expression omnibus (GEO) (www.ncbi.nlm.nih.gov/geo/). The dataset was assigned with GEO series accession number of GSE98043, which was based on the platform of GPL21575 (Agilent-070156 Human_miRNA_V21.0_Microarray 046064) using SurePrint human miRNA microarray (11).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The current bioinformatics study is based on plasma miRNA expression profiling of GDM available online in gene expression omnibus (GEO) (www.ncbi.nlm.nih.gov/geo/). The dataset was assigned with GEO series accession number of GSE98043, which was based on the platform of GPL21575 (Agilent-070156 Human_miRNA_V21.0_Microarray 046064) using SurePrint human miRNA microarray (11).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2585944", "GSM2585945", "GSM2585946", "GSM2585947"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "21575", "taxon": "Homo sapiens", "title": "Circulating miRNAs for gestational diabetes mellitus", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31497041:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:34a829184bf0def83b57d0b5dcb05ee8b8bb7b26f347e4037691447a9629150d", "bytes": 757, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[1]#A86640TBL1", "version": null, "note": "The List of Hub-Bottleneck Elements of the Protein-Protein Interaction Network Analysis from STRING Database for GDM", "structure": {"pmcid": "PMC6678685", "section_index": 4, "section_title": "4. Results", "row_count": 15, "column_count": 5}, "table": {"label": "Table 1.", "caption": "The List of Hub-Bottleneck Elements of the Protein-Protein Interaction Network Analysis from STRING Database for GDM", "rows": [["Row", "Display Name", "Degree", "BC", "Disease Score"], ["1", "INS*", "58", "0.2", "3.5"], ["2", "ALB", "44", "0.1", "1.3"], ["3", "LEP", "41", "0.04", "2.5"], ["4", "IGF1", "39", "0.03", "1.4"], ["5", "GCG", "38", "0.05", "1.5"], ["6", "ADIPOQ", "38", "0.04", "2.5"], ["7", "IL6", "36", "0.03", "1.7"], ["8", "PPARG", "35", "0.04", "1.6"], ["9", "TNF", "32", "0.05", "1.7"], ["10", "IRS1", "28", "0.01", "5"], ["11", "RETN", "28", "0.01", "1.9"], ["12", "IGF2", "23", "0.02", "1.3"], ["13", "APOB", "22", "0.008", "1.1"], ["14", "GCK", "22", "0.03", "5"]], "row_count": 15, "column_count": 5, "numeric_cells": 56, "header_rows": 1, "locator": "section[4]/table-wrap[1]#A86640TBL1"}}, {"id": "asset:table:pmid:31497041:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:768055f441992871045a32e445185dad4ffa4719d7ea871be770243727e83a98", "bytes": 801, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[4]/table-wrap[2]#A86640TBL2", "version": null, "note": "The List of Differential Expressed MicroRNAs and Their Target Genes (P ≤ 0.05)", "structure": {"pmcid": "PMC6678685", "section_index": 4, "section_title": "4. Results", "row_count": 13, "column_count": 5}, "table": {"label": "Table 2.", "caption": "The List of Differential Expressed MicroRNAs and Their Target Genes (P ≤ 0.05)", "rows": [["Row", "MicroRNAs", "Target Gene", "FC", "EP"], ["1", "hsa-miR-371a-5p", "IL6", "7.56", "D"], ["2", "hsa-miR-374b-5p", "IL6", "57.30", "D"], ["3", "hsa-miR-365a-3p", "IL6", "16.33", "U"], ["4", "hsa-miR-146b-3p", "IL6", "46.52", "U"], ["5", "hsa-miR-568", "IL6", "7.80", "U"], ["6", "hsa-miR-574-3p", "IL6", "10.62", "U"], ["7", "hsa-miR-325", "GCG", "10.05", "U"], ["8", "hsa-miR-520e", "APOB", "11.47", "U"], ["9", "hsa-miR-145-5p*", "APOB, IRS1, RETN, GCG", "37.53", "U"], ["10", "hsa-miR-609", "ALB, IGF2", "20.40", "D"], ["11", "hsa-miR-583", "ALB", "11.15", "U"], ["12", "hsa-miR-875-5p", "TNF, LEP, IRS1", "14.52", "D"]], "row_count": 13, "column_count": 5, "numeric_cells": 36, "header_rows": 1, "locator": "section[4]/table-wrap[2]#A86640TBL2"}}], "gaps": ["asset:data:geo:GSE98043 not downloaded", "asset:data:geo:GSE98043 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": 0.8, "band": "high", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": "network_analysis", "specific": "centrality", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "centrality"}}, {"id": "method-3", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Human samples of healthy controls and gestational diabetes mellitus were compared in terms of expression profiling of differentially expressed (DE)miRNA via GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r/)."}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE98043"], "resolved_accessions": ["GSE98043"], "statements": ["The current bioinformatics study is based on plasma miRNA expression profiling of GDM available online in gene expression omnibus (GEO) (www.ncbi.nlm.nih.gov/geo/). The dataset was assigned with GEO series accession number of GSE98043, which was based on the platform of GPL21575 (Agilent-070156 Human_miRNA_V21.0_Microarray 046064) using SurePrint human miRNA microarray (11)."], "basis": "The paper names GSE98043 in gene expression omnibus (GEO) and the accession resolves in the repository. 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