Identification of Hub Genes in Type 2 Diabetes Mellitus Using Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32547141", "kind": "science-record", "revision": 8, "content_hash": "sha256:b084df0c70c9faa539af1928f3b21a1f04c822ff12b7f93663a7d3be8617bccb", "created_at": "2026-11-01T15:41:03Z", "updated_at": "2026-11-01T22:01:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Hub Genes in Type 2 Diabetes Mellitus Using Bioinformatics Analysis.", "doi": "10.2147/DMSO.S245165", "pmid": "32547141", "authors": ["YiXuan Lin", "Jinju Li", "Di Wu", "FanJing Wang", "ZhaoHui Fang", "GuoMing Shen"], "journal": "Diabetes, metabolic syndrome and obesity : targets and therapy", "year": 2020, "abstract": "BACKGROUND: Type 2 diabetes mellitus (T2DM) is one of the most common chronic diseases in the world with complicated pathogenesis. This study aimed to identify differentially expressed genes (DEGs) and molecular pathways in T2DM using bioinformatics analysis.\nMATERIALS AND METHODS: To explore potential therapeutic targets for T2DM, we analyzed three microarray datasets (GSE50397, GSE38642, and GSE44035) acquired from the Gene Expression Omnibus (GEO) database. DEGs between T2DM islet and normal islet were picked out by the GEO2R tool and Venn diagram software. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to identify the pathways and functional annotation of DEGs. Then, protein-protein interaction (PPI) of these DEGs was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes/Proteins (STRING).\nRESULTS: In total, we identified 36 DEGs in the three datasets, including 32 up-regulated genes and four down-regulated genes. The improved functions and pathways of the DEGs enriched in cytokine-cytokine receptor interaction, pathways in cancer, PI3K-Akt signaling pathway, and Rheumatoid arthritis. Among them, ten hub genes with a high degree of connectivity were selected. Furthermore, via the re-analysis of DAVID, four genes (IL6, MMP3, MMP1, and IL11) were significantly enriched in the Rheumatoid arthritis pathway.\nCONCLUSION: Our study, based on the GEO database, identified four significant up-regulated DEGs and provided novel targets for diagnosis and treatment of T2DM.", "claims": [{"id": "claim-method", "statement": "The DEGs between DM and non-diabetic samples were screened using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32547141", "locator": "sections[4] \"Data Processing of DEGs\" paragraph 2", "quote": "The DEGs between DM and non-diabetic samples were screened using GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE50397 dataset contained 66 non-diabetic pancreatic islets samples and 11 diabetic pancreatic islets samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32547141", "locator": "sections[3] \"Microarray Data Information\" paragraph 2", "quote": "The GSE50397 dataset contained 66 non-diabetic pancreatic islets samples and 11 diabetic pancreatic islets samples."}], "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:32547141"], "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:GSE38642"], "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:GSE38642"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32547141", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/DMSO.S245165", "sha256": "sha256:e122b1915ac20e2180f171defc7863875768e18392929288d6e98fd5d061805b", "bytes": 22649, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/DMSO.S245165", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7250707", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE38642", "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=GSE38642", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38642", "version": null, "note": "The GSE50397 dataset contained 66 non-diabetic pancreatic islets samples and 11 diabetic pancreatic islets samples.", 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accession URL", "access_statement_verbatim": "The GSE50397 dataset contained 66 non-diabetic pancreatic islets samples and 11 diabetic pancreatic islets samples.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1077110", "GSM1077111", "GSM1077112", "GSM1077113", "GSM1077114", "GSM1077115", "GSM1077116", "GSM1077117", "GSM1077118", "GSM1077119"], "sample_count": 10, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Gene expression from human pancreatic islet", "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:GSE50397", "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=GSE50397", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, 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"GSM1218083", "GSM1218084", "GSM1218085", "GSM1218086", "GSM1218087", "GSM1218088", "GSM1218089", "GSM1218090", "GSM1218091", "GSM1218092", "GSM1218093", "GSM1218094", "GSM1218095", "GSM1218096", "GSM1218097", "GSM1218098", "GSM1218099", "GSM1218100", "GSM1218101", "GSM1218102", "GSM1218103", "GSM1218104", "GSM1218105", "GSM1218106", "GSM1218107", "GSM1218108", "GSM1218109", "GSM1218110", "GSM1218111", "GSM1218112", "GSM1218113", "GSM1218114", "GSM1218115", "GSM1218116", "GSM1218117", "GSM1218118", "GSM1218119", "GSM1218120", "GSM1218121", "GSM1218122", "GSM1218123", "GSM1218124", "GSM1218125", "GSM1218126", "GSM1218127", "GSM1218128", "GSM1218129", "GSM1218130", "GSM1218131", "GSM1218132", "GSM1218133", "GSM1218134", "GSM1218135", "GSM1218136"], "sample_count": 89, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Global transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism [expression 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wide variety of inflammation associated disease states", "25"], ["MMP3", "Matrix metallopeptidase 3", "MMP3 can involve in the breakdown of extracellular matrix", "23"], ["INHBA", "Inhibin subunit beta A", "INHBA may involve in regulating insulin secretion", "20"], ["MMP1", "Matrix metallopeptidase 1", "MMP1 may related to tumor-induced angiogenesis.", "20"], ["VCAN", "Versican core protein", "VCAN is involved in cell adhesion, proliferation, proliferation migration and angiogenesis", "19"], ["FGF7", "Fibroblast growth factor 7", "FGF7 Plays an important role in the regulation of embryonic development, cell proliferation and cell differentiation", "19"], ["PDGFRA", "Platelet derived growth factor receptor alpha", "PDGFRA plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemo taxis", "19"], ["THBS2", "Thrombospondin 2", "THBS2 can mediates cell-to-cell and cell-to-matrix interactions, inhibit angiogenesis.", "18"], ["IL11", "Interleukin-11", "IL11 can support the proliferation of hematopoietic stem cells and megakaryocyte progenitor cells.", "18"], ["CYR61", "Cysteine rich angiogenic inducer 61", "CYR61 may involve in angiogenesis, inflammation and matrix remodeling", "17"]], "row_count": 11, "column_count": 4, "numeric_cells": 21, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T0004"}}, {"id": "asset:table:pmid:32547141:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:597afe7b2251898bbc8c7f4ee2b8fe96f4cf5930f3e38e4b70e656fdb9e60e3b", "bytes": 552, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#T0001", "version": null, "note": "36 Differentially Expressed Genes (DEGs) Were Detected from Three Datasets, Including 32 Up-Regulated Genes and 4 Down-Regulated Genes", "structure": {"pmcid": "PMC7250707", "section_index": 8, "section_title": "Identification of DEGs in DM", "row_count": 3, "column_count": 2}, "table": {"label": "Table 1", "caption": "36 Differentially Expressed Genes (DEGs) Were Detected from Three Datasets, Including 32 Up-Regulated Genes and 4 Down-Regulated Genes", "rows": [["DEGs", "Genes Name"], ["Up-regulated", "GJA1 CCL22 GFPT2 RASD2 IL24 BDKRB1 LTBP1 ABCA8 SPON1 NT5E ABI3BPSFRP4 SRGN MMP1 IL6 MFAP4 MMP3 FGF7 CEMIP THBS2 CYTIP TGFA IL7RVCAN IL33 CXCL5 PDGFRA IL11 SLIT2 MMP10 CYR61 INHBA"], ["Down-regulated", "CACNA2D1 WNT4 MCF2L2 INPP5F"]], "row_count": 3, "column_count": 2, "numeric_cells": 1, "header_rows": 1, "locator": "section[8]/table-wrap[1]#T0001"}}, {"id": "asset:table:pmid:32547141:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:30af385ede99e8fc2237c253da0401d7aa62bd78279e6b93d517c47e6537e93c", "bytes": 1590, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#T0002", "version": null, "note": "Gene Ontology Analysis of Differentially Expressed Genes in T2DM", "structure": {"pmcid": "PMC7250707", "section_index": 9, "section_title": "GO and KEGG Enrichment Analyses", "row_count": 19, "column_count": 4}, "table": {"label": "Table 2", "caption": "Gene Ontology Analysis of Differentially Expressed Genes in T2DM", "rows": [["Category", "Term", "Count", "P-value"], ["GOTERM_CC_DIRECT", "GO:0005576~extracellular region", "22", "1.97E-14"], ["GOTERM_CC_DIRECT", "GO:0005615~extracellular space", "16", "4.82E-09"], ["GOTERM_CC_DIRECT", "GO:0005578~proteinaceous extracellular matrix", "9", "2.57E-08"], ["GOTERM_CC_DIRECT", "GO:0031012~extracellular matrix", "9", "5.54E-08"], ["GOTERM_CC_DIRECT", "GO:0009986~cell surface", "5", "1.77E-02"], ["GOTERM_CC_DIRECT", "GO:0001527~microfibril", "2", "1.85E-02"], ["GOTERM_MF_DIRECT", "GO:0008201~heparin binding", "5", "3.24E-04"], ["GOTERM_MF_DIRECT", "GO:0008083~growth factor activity", "5", "3.39E-04"], ["GOTERM_MF_DIRECT", "GO:0005125~cytokine activity", "5", "4.65E-04"], ["GOTERM_MF_DIRECT", "GO:0005509~calcium ion binding", "7", "3.25E-03"], ["GOTERM_MF_DIRECT", "GO:0004222~metalloendopeptidase activity", "3", "2.29E-02"], ["GOTERM_MF_DIRECT", "GO:0005540~hyaluronic acid binding", "2", "4.66E-02"], ["GOTERM_BP_DIRECT", "GO:0007267~cell-cell signaling", "6", "1.71E-04"], ["GOTERM_BP_DIRECT", "GO:0045669~positive regulation of osteoblast differentiation", "4", "2.62E-04"], ["GOTERM_BP_DIRECT", "GO:0008284~positive regulation of cell proliferation", "7", "3.62E-04"], ["GOTERM_BP_DIRECT", "GO:0042060~wound healing", "4", "6.11E-04"], ["GOTERM_BP_DIRECT", "GO:0030308~negative regulation of cell growth", "4", "2.02E-03"], ["GOTERM_BP_DIRECT", "GO:0010628~positive regulation of gene expression", "5", "2.07E-03"]], "row_count": 19, "column_count": 4, "numeric_cells": 54, "header_rows": 1, "locator": "section[9]/table-wrap[1]#T0002"}}, {"id": "asset:table:pmid:32547141:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d2925d2ed6e3ec62ac860bfdac9d7b06443ece478588f40d61f49463f6cf948", "bytes": 894, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#T0003", "version": null, "note": "The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis in T2DM", "structure": {"pmcid": "PMC7250707", "section_index": 9, "section_title": "GO and KEGG Enrichment Analyses", "row_count": 7, "column_count": 5}, "table": {"label": "Table 3", "caption": "The Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis in T2DM", "rows": [["Category", "Term", "Count", "P-value", "Genes"], ["KEGG_PATHWAY", "hsa04060: Cytokine–cytokine receptor interaction", "7", "1.44E-04", "INHBA, IL6, CCL22, CXCL5, IL24, IL7R, IL11"], ["KEGG_PATHWAY", "hsa05323: Rheumatoid arthritis", "5", 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"Function and Connectivity of the Ten Hub Genes", "structure": {"pmcid": "PMC7250707", "section_index": 10, "section_title": "PPI Network and CytoHubba Analysis", "row_count": 11, "column_count": 4}, "table": {"label": "Table 4", "caption": "Function and Connectivity of the Ten Hub Genes", "rows": [["Gene Symbol", "Gene Description", "Function", "Degree"], ["IL6", "Interleukin-6", "IL6 is implicated in a wide variety of inflammation associated disease states", "25"], ["MMP3", "Matrix metallopeptidase 3", "MMP3 can involve in the breakdown of extracellular matrix", "23"], ["INHBA", "Inhibin subunit beta A", "INHBA may involve in regulating insulin secretion", "20"], ["MMP1", "Matrix metallopeptidase 1", "MMP1 may related to tumor-induced angiogenesis.", "20"], ["VCAN", "Versican core protein", "VCAN is involved in cell adhesion, proliferation, proliferation migration and angiogenesis", "19"], ["FGF7", "Fibroblast growth factor 7", "FGF7 Plays an important role in the regulation of embryonic development, cell proliferation and cell differentiation", "19"], ["PDGFRA", "Platelet derived growth factor receptor alpha", "PDGFRA plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemo taxis", "19"], ["THBS2", "Thrombospondin 2", "THBS2 can mediates cell-to-cell and cell-to-matrix interactions, inhibit angiogenesis.", "18"], ["IL11", "Interleukin-11", "IL11 can support the proliferation of hematopoietic stem cells and megakaryocyte progenitor cells.", "18"], ["CYR61", "Cysteine rich angiogenic inducer 61", "CYR61 may involve in angiogenesis, inflammation and matrix remodeling", "17"]], "row_count": 11, "column_count": 4, "numeric_cells": 21, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T0004"}}, {"id": "asset:table:pmid:32547141:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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