Investigation of mechanisms of mesenchymal stem cells for treatment of diabetic nephropathy via construction of a miRNA-TF-mRNA network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29532746", "kind": "science-record", "revision": 9, "content_hash": "sha256:2e45a33008afce3607ca4c19bdbb2a290bf8b67b9f98347adee2d8999848bc4d", "created_at": "2026-11-01T15:40:32Z", "updated_at": "2026-11-01T22:43:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of mechanisms of mesenchymal stem cells for treatment of diabetic nephropathy via construction of a miRNA-TF-mRNA network.", "doi": "10.1080/0886022X.2017.1421556", "pmid": "29532746", "authors": ["Hailing Yang", "Xiaofei Zhang", "Guangda Xin"], "journal": "Renal failure", "year": 2018, "abstract": "BACKGROUND: Recent studies have reported that mesenchymal stem cells (MSCs) exert therapeutic effects on the treatment of diabetic nephropathy (DN), but the underlying mechanisms remain unclear.\nMETHODS: A dataset GSE65561 was obtained from Gene Expression Omnibus (GEO) database, which contained four healthy control samples (group 1), four healthy controls samples co-cultured with MSCs (group 2), five DN samples (group 3) and five DN samples co-cultured with MSCs (group 4). The differentially expressed genes (DEGs) between group 3 vs. group 1 and group 4 vs. group 2 were constructed using Linear Models for Microarray (LIMMA) package package. Then, DAVID was used to analyze the functional enrichment of DEGs. Based on STRING database the protein-protein interaction (PPI) network was visualized by the Cytoscape plug-in CytoNCA. Besides, the hub miRNAs and transcription factors (TFs) regulating DEGs were predicted using Webgestalt.\nRESULTS: Totally, 303 up-regulated and 88 down-regulated DEGs were shared in group 3 vs. group 1 and group 4 vs. group 2. Besides, the up-regulated DEGs were mainly enriched in 'translation' and 'translational elongation', while the down-regulated genes were only enriched in 'protein kinase activity'. RPS27A and RPLP0 had a higher degree in the PPI network and they were regulated by EIF3M. In addition, ETF1 was predicted to be an important gene, which was regulated by miR-150, miR-134 and EIF2S1.\nCONCLUSIONS: RPS27A, RPLP0 and ETF1 may be potential targets for MSCs on the treatment of DN. Highlights RPS27A and RPLP0 may be important genes in the treatment of MSCs for DN. TF EIF3M may play a key role in the treatment of MSCs for DN. MiR-150 and miR-134 may be essential microRNAs in the treatment of MSCs for DN.", "claims": [{"id": "claim-method", "statement": "The DEGs in the comparison groups of group 3 vs. group 1 and group 4 vs. group 2 were identified by Linear Models for Microarray (LIMMA) package (Version: 3.30.3) [17] in R software and the t-test was used to calculate p values of each DEG.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29532746", "locator": "sections[4] \"Identification of DEGs shared in group 3 vs. group 1 and group 4 vs. group 2\" paragraph 2", "quote": "The DEGs in the comparison groups of group 3 vs. group 1 and group 4 vs. group 2 were identified by Linear Models for Microarray (LIMMA) package (Version: 3.30.3) [17] in R software and the t-test was used to calculate p values of each DEG."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray expression data and platform annotation files of GSE65561 [11] uploaded in Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65561) were obtained and it was sequenced from the chip platform GPL16686 [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]. A total of 18 cell samples were included in this dataset, four healthy control samples (group 1), four healthy controls samples co-cultured with MSCs for 48 h (group 2), five samples from type 2 diabetic patients with end-stage renal disease groups (group 3) and five samples of diabetic patients with end-stage renal disease groups co-cultured with MSCs for 48 h (group 4).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29532746", "locator": "sections[3] \"Microarray data acquisition\" paragraph 2", "quote": "The microarray expression data and platform annotation files of GSE65561 [11] uploaded in Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65561) were obtained and it was sequenced from the chip platform GPL16686 [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]. A total of 18 cell samples were included in this dataset, four healthy control samples (group 1), four healthy controls samples co-cultured with MSCs for 48 h (group 2), five samples from type 2 diabetic patients with end-stage renal disease groups (group 3) and five samples of diabetic patients with end-stage renal disease groups co-cultured with MSCs for 48 h (group 4)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study obtained GSE65561 from the GEO database and identified shared DEGs between group 3 vs. group 1 and group 4 vs. group 2 using RMA normalization and the LIMMA package, with t-test p-values < .05.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29532746", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Methods: A dataset GSE65561 was obtained from Gene Expression Omnibus (GEO) database, which contained four healthy control samples (group 1), four healthy controls samples co-cultured with MSCs (group 2), five DN samples (group 3) and five DN samples co-cultured with MSCs (group 4). The differentially expressed genes (DEGs) between group 3 vs. group 1 and group 4 vs. group 2 were constructed using Linear Models for Microarray (LIMMA) package package."}, {"asset": "source:pmid:29532746", "locator": "sections[4] \"Identification of DEGs shared in group 3 vs. group 1 and group 4 vs. group 2\" paragraph 2", "quote": "The GSE65561 chip data was normalized using the robust multi-array average (RMA) method [16] in the Affy package (Version: 1.52.0) of the R software (Version: 3.3.2). The DEGs in the comparison groups of group 3 vs. group 1 and group 4 vs. group 2 were identified by Linear Models for Microarray (LIMMA) package (Version: 3.30.3) [17] in R software and the t-test was used to calculate p values of each DEG. p values < .05 was used as the threshold."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study obtained GSE65561 from the GEO database and identified shared DEGs between group 3 vs. group 1 and group 4 vs. group 2 using RMA normalization and the LIMMA package, with t-test p-values < .05.", "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:29532746"], "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:GSE65561"], "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:GSE65561"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29532746", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1080/0886022X.2017.1421556", "sha256": "sha256:6c688daeec866128130ffe83499fb4d5032807c599c515f3955ef16f15da8633", "bytes": 25897, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1080/0886022X.2017.1421556", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6014302", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE65561", "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=GSE65561", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE65561", "version": null, "note": "The microarray expression data and platform annotation files of GSE65561 [11] uploaded in Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65561) were obtained and it was sequenced from the chip platform GPL16686 [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]. A total of 18 cell samples were included in this dataset, four healthy control samples (group 1), four healthy controls samples co-cultured with MSCs for 48 h (group 2), five samples from type 2 diabetic patients with end-stage renal disease groups (group 3) and five samples of diabetic patients with end-stage renal disease groups co-cultured with MSCs for 48 h (group 4).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The microarray expression data and platform annotation files of GSE65561 [11] uploaded in Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65561) were obtained and it was sequenced from the chip platform GPL16686 [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]. A total of 18 cell samples were included in this dataset, four healthy control samples (group 1), four healthy controls samples co-cultured with MSCs for 48 h (group 2), five samples from type 2 diabetic patients with end-stage renal disease groups (group 3) and five samples of diabetic patients with end-stage renal disease groups co-cultured with MSCs for 48 h (group 4).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1600118", "GSM1600119", "GSM1600120", "GSM1600121", "GSM1600122", "GSM1600123", "GSM1600124", "GSM1600125", "GSM1600126", "GSM1600127", "GSM1600128", "GSM1600129", "GSM1600130", "GSM1600131", "GSM1600132", "GSM1600133", "GSM1600134", "GSM1600135"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "16686", "taxon": "Homo sapiens", "title": "Expression data from MSC-treated monocytes", "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:29532746:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2ac4f089b9e613319eed540f277b239ae95faef8aa7eed1fa6d3be8c6d2bceff", "bytes": 5158, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#t0001", "version": null, "note": "Results of enrichment analysis of DEGs.", "structure": {"pmcid": "PMC6014302", "section_index": 12, "section_title": "Functional enrichment analysis of the DEGs", "row_count": 27, "column_count": 4}, "table": {"label": "Table 1.", "caption": "Results of enrichment analysis of DEGs.", "rows": [["Terms", "Count", "p value", "Genes"], ["Up-regulated genes enriching BP", "", "", ""], ["GO:0006412∼translation", "33", "1.23E-16", "MRPS16, PABPC4, MRPS10, RPS15A, RPL13AP20, DTD1, RPL21P28, RPS3, MRPL11, EIF3G, RPL9, RPLP0, EIF1AY, RPL26L1, MRPL37, EIF3I, EIF3M, RPS27A, MRPL35, RPL36AL, EEF1A1, RPSAP19, RPL27, RPS9, MRPS21, MRPS7, ETF1, RPS5, RPS19, MRPL27, RPS14, EIF2S1, MRPL47"], ["GO:0006414∼translational elongation", "14", "6.47E-9", "EEF1A1, RPSAP19, RPS9, RPL27, RPS15A, RPS5, RPS3, RPL21P28, RPS19, RPLP0, RPL9, RPS14, RPL26L1, RPS27A"], ["GO:0006119∼oxidative phosphorylation", "12", "4.03E-7", "NDUFB3, NDUFB5, UQCR11, NDUFB7, NDUFAB1, ATP5F1, NDUFS2, ATP5H, ATP5G3, NDUFS1, ATP6V1F, UQCRHL"], ["GO:0031397∼negative regulation of protein ubiquitination", "10", "2.38E-6", "PSMB7, GTPBP4, PSMB6, PSMC5, PSMB1, PSMA5, PSME3, PSMB8, RPS27A, PSMB9"], ["GO:0031400∼negative regulation of protein modification process", "12", "2.84E-6", "PSMB7, GTPBP4, PSMB6, PSMC5, PSMB1, PSMA5, NLRP12, PEBP1, PSME3, PSMB8, RPS27A, PSMB9"], ["Up-regulated genes enriching CC", "", "", ""], ["GO:0005840∼ribosome", "27", "3.98E-16", "MRPS16, MRPS10, RPS15A, RPL13AP20, RPL21P28, RPS3, MRPL11, RPLP0, RPL9, RPL26L1, MRPL54, MRPL37, RPS27A, MRPL35, RPL36AL, RPSAP19, MRPS23, RPS9, RPL27, MRPS21, MRPS7, RPS5, RPS19, MRPL27, RPS14, MRPL47, MRPL46"], ["GO:0030529∼ribonucleoprotein complex", "38", "5.29E-15", "MRPS16, STRAP, PABPC4, CWC15, SNRPD1, MRPS10, RPS15A, RPL13AP20, SF3B4, RPL21P28, RPS3, MRPL11, RPL9, RPLP0, RPL26L1, MRPL54, PPIL3, MRPL37, LSM3, RPS27A, MRPL35, RPL36AL, BCAS2, TXNL4B, RPSAP19, MRPS23, RPL27, RPS9, MRPS21, MRPS7, RPS5, RPS19, MRPL27, RPS14, EIF2S1, MRPL47, POP4, MRPL46"], ["GO:0044429∼mitochondrial part", "39", "9.30E-14", "NDUFB3, MRPS16, NDUFB5, NDUFB7, COX7B, NDUFAB1, TIMM10, ECHS1, TIMM50, TIMM13, SFXN2, COX5A, ATP5G3, DTD1, MRPL11, ACSL1, UQCR11, PARL, COX6B1, MRPL37, ATP5H, NDUFS2, NDUFS1, MRPL35, ACAA2, SLC25A5, SLC25A6, ATP5F1, COX4I1, MRPS21, TIMM8B, UQCRHL, PPIF, MRPL27, PEBP1, MRPL47, TOMM22, PMPCA, SURF1"], ["GO:0005743∼mitochondrial inner membrane", "28", "2.97E-13", "NDUFB3, NDUFB5, NDUFB7, COX7B, TIMM10, NDUFAB1, TIMM50, TIMM13, SFXN2, COX5A, ATP5G3, UQCR11, PARL, COX6B1, NDUFS2, ATP5H, NDUFS1, ACAA2, SLC25A5, SLC25A6, ATP5F1, COX4I1, TIMM8B, UQCRHL, PPIF, TOMM22, SURF1, PMPCA"], ["GO:0005739∼mitochondrion", "52", "5.69E-13", "GM2A, NDUFAB1, TIMM50, COX5A, C14ORF2, MTHFD2, UQCR11, PARL, MRPL37, ATP5H, NDUFS2, NDUFS1, MRPL35, ACAA2, SLC25A5, SLC25A6, COX4I1, MRPS7, TIMM8B, TMEM186, PEBP1, MRPL47, TOMM22, PMPCA, SURF1, MRPL46, NDUFB3, MRPS16, NDUFB5, NAPG, NDUFB7, COX7B, TIMM10, MRPS10, ECHS1, CHCHD2, TIMM13, SFXN2, ATP5G3, DTD1, MRPL11, ACSL1, MRPL54, COX6B1, MRPS23, ATP5F1, MRPS21, UQCRHL, PPIF, MRPL27, ALKBH3, VPS25"], ["Up-regulated genes enriching MF", "", "", ""], ["GO:0003735∼structural constituent of ribosome", "24", "5.92E-16", "RPSAP19, MRPS16, MRPS10, RPS15A, RPS9, RPL27, MRPS21, RPL13AP20, MRPS7, RPS5, RPS3, RPL21P28, MRPL11, RPS19, MRPL27, RPS14, RPL9, RPLP0, RPL26L1, MRPL37, MRPL47, RPS27A, MRPL35, RPL36AL"], ["GO:0015078∼hydrogenion transmembrane transporter activity", "11", "9.80E-7", "UQCR11, COX7B, COX6B1, ATP5F1, COX4I1, COX5A, SURF1, ATP5H, ATP5G3, ATP6V1F, UQCRHL"], ["GO:0005198∼structural molecule activity", "28", "1.02E-6", "MRPS16, MRPS10, RPS15A, RPL13AP20, TPM4, RPL21P28, RPS3, MRPL11, RPLP0, RPL9, RPL26L1, TUBB6, MRPL37, RPS27A, MRPL35, RPL36AL, RPSAP19, RPS9, RPL27, MRPS21, MRPS7, EMILIN2, RPS5, RPS19, MRPL27, RPS14, MRPL47, LAMC1"], ["GO:0003723∼RNA binding", "29", "3.53E-6", "CNBP, PABPC4, CWC15, SNRPD1, RPS15A, TIMM50, SF3B4, RPL21P28, RPS3, MRPL11, EIF3G, RPLP0, RPL9, NUDT21, EIF1AY, LSM3, NXF3, RPS9, MRPS7, ETF1, CRYZ, RPS5, RPS19, ABT1, RPS14, EIF2S1, PSPC1, CIRBP, POP4"], ["GO:0015077∼monovalent inorganic cation transmembrane transporter activity", "11", "3.73E-6", "UQCR11, COX7B, COX6B1, ATP5F1, COX4I1, COX5A, SURF1, ATP5H, ATP5G3, ATP6V1F, UQCRHL"], ["Up-regulated genes enriching pathway", "", "", ""], ["hsa05012:Parkinson's disease", "17", "1.96E-9", "NDUFB3, NDUFB5, NDUFB7, SLC25A5, SLC25A6, COX7B, ATP5F1, NDUFAB1, COX4I1, COX5A, ATP5G3, UQCRHL, UQCR11, COX6B1, NDUFS2, ATP5H, NDUFS1"], ["hsa00190:Oxidative phosphorylation", "16", "2.02E-8", "NDUFB3, NDUFB5, NDUFB7, COX7B, ATP5F1, NDUFAB1, COX4I1, COX5A, ATP5G3, UQCRHL, ATP6V1F, UQCR11, COX6B1, NDUFS2, ATP5H, NDUFS1"], ["hsa05016:Huntington's disease", "18", "4.42E-8", "NDUFB3, NDUFB5, NDUFB7, SLC25A5, SLC25A6, AP2S1, COX7B, ATP5F1, NDUFAB1, COX4I1, COX5A, ATP5G3, UQCRHL, UQCR11, COX6B1, NDUFS2, ATP5H, NDUFS1"], ["hsa03010:Ribosome", "13", "8.01E-8", "RPSAP19, RPS9, RPL27, RPS15A, RPS5, RPS3, RPL21P28, RPS19, RPLP0, RPL9, RPL26L1, RPS27A, RPL36AL"], ["hsa05010:Alzheimer's disease", "15", "2.47E-6", "NDUFB3, NDUFB5, NDUFB7, COX7B, ATP5F1, NDUFAB1, COX4I1, COX5A, ATP5G3, UQCRHL, UQCR11, COX6B1, NDUFS2, ATP5H, NDUFS1"], ["Down-regulated genes", "", "", ""], ["GO:0004672∼protein kinase activity", "6", "0.037", "TYK2, FASTKD1, ITGAE, PDK4, MAP3K8, MAP3K12"]], "row_count": 27, "column_count": 4, "numeric_cells": 84, "header_rows": 1, "locator": "section[12]/table-wrap[1]#t0001"}}, {"id": "asset:table:pmid:29532746:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e585b387dc608a85f15235b46c96e3d882b2c6d1f378aeb761c445b0de4a0b82", "bytes": 1016, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t0002", "version": null, "note": "Genes with node degree greater than 20 in PPI network.", "structure": {"pmcid": "PMC6014302", "section_index": 13, "section_title": "Analysis of PPI network", "row_count": 19, "column_count": 4}, "table": {"label": "Table 2.", "caption": "Genes with node degree greater than 20 in PPI network.", "rows": [["Gene", "Degree", "Betweenness", "Closeness"], ["RPS27A", "37.0", "3961.025", "0.046830755"], ["RPLP0", "34.0", "1496.081", "0.046871595"], ["RPL26L1", "34.0", "962.4223", "0.04664786"], ["RPS3", "34.0", "1346.5127", "0.046749294"], ["RPL9", "32.0", "980.9833", "0.046718817"], ["RPS15A", "31.0", "689.46735", "0.046769634"], ["RPS14", "30.0", "1155.3206", "0.04668838"], ["RPS5", "30.0", "1379.4094", "0.046728972"], ["RPL27", "30.0", "888.37836", "0.046597313"], ["SNU13", "29.0", "4506.537", "0.04646639"], ["RPS19", "27.0", "831.52124", "0.046718817"], ["MRPS7", "26.0", "2373.208", "0.04678999"], ["EEF1A1", "24.0", "3594.4336", "0.046830755"], ["RPS9", "24.0", "167.19829", "0.04642626"], ["MRPS10", "23.0", "181.42064", "0.046406217"], ["NIFK", "23.0", "1317.9271", "0.046306267"], ["MRPL11", "21.0", "285.20667", "0.04619682"], ["RPL36AL", "21.0", "237.57062", "0.04621668"]], "row_count": 19, "column_count": 4, "numeric_cells": 64, "header_rows": 1, "locator": "section[13]/table-wrap[1]#t0002"}}], "gaps": ["asset:data:geo:GSE65561 not downloaded", "asset:data:geo:GSE65561 licence not read"]}, "analysis": {"state": "complete", "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": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DEGs in the comparison groups of group 3 vs. group 1 and group 4 vs. group 2 were identified by Linear Models for Microarray (LIMMA) package (Version: 3.30.3) [17] in R software and the t-test was used to calculate p values of each DEG."}}, {"id": "method-2", "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"}}, {"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": 0.8, "band": "high", "quote": "pathway enrichment"}}], "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": ["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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE65561"], "resolved_accessions": ["GSE65561"], "statements": ["The microarray expression data and platform annotation files of GSE65561 [11] uploaded in Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE65561) were obtained and it was sequenced from the chip platform GPL16686 [HuGene-2_0-st] Affymetrix Human Gene 2.0 ST Array [transcript (gene) version]. A total of 18 cell samples were included in this dataset, four healthy control samples (group 1), four healthy controls samples co-cultured with MSCs for 48 h (group 2), five samples from type 2 diabetic patients with end-stage renal disease groups (group 3) and five samples of diabetic patients with end-stage renal disease groups co-cultured with MSCs for 48 h (group 4)."], "basis": "The paper names GSE65561 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:29532746", "data:geo:GSE65561", "asset:table:pmid:29532746:1", "asset:table:pmid:29532746:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE65561"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:52Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 56698, "completion_tokens": 4570, "cached_tokens": 2072}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:29532746", "type": "paper", "label": "pmid:29532746"}, {"id": "source:pmid:29532746", "type": "manuscript", "label": "PMID 29532746 full text"}, {"id": "data:geo:GSE65561", "type": "dataset", "label": "GEO GSE65561"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29532746", "type": "paper", "label": "pmid:29532746"}, {"id": "source:pmid:29532746", "type": "manuscript", "label": "PMID 29532746 full text"}, {"id": "data:geo:GSE65561", "type": "dataset", "label": "GEO GSE65561"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29532746", "type": "extraction", "used": ["source:pmid:29532746"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE65561", "type": "accession_resolution", "used": ["data:geo:GSE65561"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:29532746", "parent_hash": "sha256:0eac7545a9a92bc6bb18cfbec9e5b4183945c945e9c27f440c884af9cf4093db", "fork_of": null, "generation": 8}, "gaps": ["asset:data:geo:GSE65561 licence not read", "asset:data:geo:GSE65561 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["(group 1), four healthy controls samples co-cultured with MSCs (group 2), five DN samples (group 3) an", "DN samples (group 3) and five DN samples co-cultured with MSCs (group 4). The differentially expressed"], "order_basis": "paper_text_order:463", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["p 2 were constructed using Linear Models for Microarray (LIMMA) package package. Then, DAVID was use"], "order_basis": "paper_text_order:706", "id": "assay:2"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The DEGs in the comparison groups of group 3 vs. group 1 and group 4 vs. group 2 were identified by Linear Models for Microarray (LIMMA) package (Version: 3.30.3) [17] in R software and the t-test was used to calculate p values of each DEG."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}