Analysis of key genes and their functions in placental tissue of patients with gestational diabetes mellitus
This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). The GSE70493 dataset used for this study was obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in the placental tissue of women with...
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Published in | Reproductive biology and endocrinology Vol. 17; no. 1; p. 104 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
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29.11.2019
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Abstract | This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM).
The GSE70493 dataset used for this study was obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in the placental tissue of women with GDM in relation to the control tissue samples were identified and submitted to protein-protein interaction (PPI) network analysis and subnetwork module mining. Functional enrichment analyses of the PPI network and subnetworks were subsequently carried out. Finally, the integrated miRNA-transcription factor (TF)-DEG regulatory network was analyzed.
In total, 238 DEGs were identified, of which 162 were upregulated and 76 were downregulated. Through PPI network construction, 108 nodes and 278 gene pairs were obtained, from which chemokine (C-X-C motif) ligand 9 (CXCL9), CXCL10, protein tyrosine phosphatase, receptor type C (PTPRC), and human leukocyte antigen (HLA) were screened out as hub genes. Moreover, genes associated with the immune-related pathway and immune responses were found to be significantly enriched in the process of GDM. Finally, miRNAs and TFs that target the DEGs were predicted.
Four candidate genes (viz., CXCL9, CXCL10, PTPRC, and HLA) are closely related to GDM. miR-223-3p, miR-520, and thioredoxin-binding protein may play important roles in the pathogenesis of this disease. |
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AbstractList | Abstract
Background
This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM).
Methods
The GSE70493 dataset used for this study was obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in the placental tissue of women with GDM in relation to the control tissue samples were identified and submitted to protein-protein interaction (PPI) network analysis and subnetwork module mining. Functional enrichment analyses of the PPI network and subnetworks were subsequently carried out. Finally, the integrated miRNA–transcription factor (TF)–DEG regulatory network was analyzed.
Results
In total, 238 DEGs were identified, of which 162 were upregulated and 76 were downregulated. Through PPI network construction, 108 nodes and 278 gene pairs were obtained, from which chemokine (C-X-C motif) ligand 9 (
CXCL9
),
CXCL10
, protein tyrosine phosphatase, receptor type C (
PTPRC
), and human leukocyte antigen (
HLA
) were screened out as hub genes. Moreover, genes associated with the immune-related pathway and immune responses were found to be significantly enriched in the process of GDM. Finally, miRNAs and TFs that target the DEGs were predicted.
Conclusions
Four candidate genes (viz.,
CXCL9
,
CXCL10
,
PTPRC
, and
HLA
) are closely related to GDM.
miR-223-3p
,
miR-520
, and thioredoxin-binding protein may play important roles in the pathogenesis of this disease. This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). The GSE70493 dataset used for this study was obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in the placental tissue of women with GDM in relation to the control tissue samples were identified and submitted to protein-protein interaction (PPI) network analysis and subnetwork module mining. Functional enrichment analyses of the PPI network and subnetworks were subsequently carried out. Finally, the integrated miRNA-transcription factor (TF)-DEG regulatory network was analyzed. In total, 238 DEGs were identified, of which 162 were upregulated and 76 were downregulated. Through PPI network construction, 108 nodes and 278 gene pairs were obtained, from which chemokine (C-X-C motif) ligand 9 (CXCL9), CXCL10, protein tyrosine phosphatase, receptor type C (PTPRC), and human leukocyte antigen (HLA) were screened out as hub genes. Moreover, genes associated with the immune-related pathway and immune responses were found to be significantly enriched in the process of GDM. Finally, miRNAs and TFs that target the DEGs were predicted. Four candidate genes (viz., CXCL9, CXCL10, PTPRC, and HLA) are closely related to GDM. miR-223-3p, miR-520, and thioredoxin-binding protein may play important roles in the pathogenesis of this disease. Background This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). Methods The GSE70493 dataset used for this study was obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in the placental tissue of women with GDM in relation to the control tissue samples were identified and submitted to protein-protein interaction (PPI) network analysis and subnetwork module mining. Functional enrichment analyses of the PPI network and subnetworks were subsequently carried out. Finally, the integrated miRNA-transcription factor (TF)-DEG regulatory network was analyzed. Results In total, 238 DEGs were identified, of which 162 were upregulated and 76 were downregulated. Through PPI network construction, 108 nodes and 278 gene pairs were obtained, from which chemokine (C-X-C motif) ligand 9 (CXCL9), CXCL10, protein tyrosine phosphatase, receptor type C (PTPRC), and human leukocyte antigen (HLA) were screened out as hub genes. Moreover, genes associated with the immune-related pathway and immune responses were found to be significantly enriched in the process of GDM. Finally, miRNAs and TFs that target the DEGs were predicted. Conclusions Four candidate genes (viz., CXCL9, CXCL10, PTPRC, and HLA) are closely related to GDM. miR-223-3p, miR-520, and thioredoxin-binding protein may play important roles in the pathogenesis of this disease. Keywords: Gestational diabetes mellitus, Differentially expressed genes, Protein-protein interaction network, Integrated regulatory network, Transcription factors Background This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). Methods The GSE70493 dataset used for this study was obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in the placental tissue of women with GDM in relation to the control tissue samples were identified and submitted to protein-protein interaction (PPI) network analysis and subnetwork module mining. Functional enrichment analyses of the PPI network and subnetworks were subsequently carried out. Finally, the integrated miRNA–transcription factor (TF)–DEG regulatory network was analyzed. Results In total, 238 DEGs were identified, of which 162 were upregulated and 76 were downregulated. Through PPI network construction, 108 nodes and 278 gene pairs were obtained, from which chemokine (C-X-C motif) ligand 9 (CXCL9), CXCL10, protein tyrosine phosphatase, receptor type C (PTPRC), and human leukocyte antigen (HLA) were screened out as hub genes. Moreover, genes associated with the immune-related pathway and immune responses were found to be significantly enriched in the process of GDM. Finally, miRNAs and TFs that target the DEGs were predicted. Conclusions Four candidate genes (viz., CXCL9, CXCL10, PTPRC, and HLA) are closely related to GDM. miR-223-3p, miR-520, and thioredoxin-binding protein may play important roles in the pathogenesis of this disease. This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). The GSE70493 dataset used for this study was obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in the placental tissue of women with GDM in relation to the control tissue samples were identified and submitted to protein-protein interaction (PPI) network analysis and subnetwork module mining. Functional enrichment analyses of the PPI network and subnetworks were subsequently carried out. Finally, the integrated miRNA-transcription factor (TF)-DEG regulatory network was analyzed. In total, 238 DEGs were identified, of which 162 were upregulated and 76 were downregulated. Through PPI network construction, 108 nodes and 278 gene pairs were obtained, from which chemokine (C-X-C motif) ligand 9 (CXCL9), CXCL10, protein tyrosine phosphatase, receptor type C (PTPRC), and human leukocyte antigen (HLA) were screened out as hub genes. Moreover, genes associated with the immune-related pathway and immune responses were found to be significantly enriched in the process of GDM. Finally, miRNAs and TFs that target the DEGs were predicted. Four candidate genes (viz., CXCL9, CXCL10, PTPRC, and HLA) are closely related to GDM. miR-223-3p, miR-520, and thioredoxin-binding protein may play important roles in the pathogenesis of this disease. BACKGROUNDThis study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). METHODSThe GSE70493 dataset used for this study was obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in the placental tissue of women with GDM in relation to the control tissue samples were identified and submitted to protein-protein interaction (PPI) network analysis and subnetwork module mining. Functional enrichment analyses of the PPI network and subnetworks were subsequently carried out. Finally, the integrated miRNA-transcription factor (TF)-DEG regulatory network was analyzed. RESULTSIn total, 238 DEGs were identified, of which 162 were upregulated and 76 were downregulated. Through PPI network construction, 108 nodes and 278 gene pairs were obtained, from which chemokine (C-X-C motif) ligand 9 (CXCL9), CXCL10, protein tyrosine phosphatase, receptor type C (PTPRC), and human leukocyte antigen (HLA) were screened out as hub genes. Moreover, genes associated with the immune-related pathway and immune responses were found to be significantly enriched in the process of GDM. Finally, miRNAs and TFs that target the DEGs were predicted. CONCLUSIONSFour candidate genes (viz., CXCL9, CXCL10, PTPRC, and HLA) are closely related to GDM. miR-223-3p, miR-520, and thioredoxin-binding protein may play important roles in the pathogenesis of this disease. Abstract Background This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). Methods The GSE70493 dataset used for this study was obtained from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) in the placental tissue of women with GDM in relation to the control tissue samples were identified and submitted to protein-protein interaction (PPI) network analysis and subnetwork module mining. Functional enrichment analyses of the PPI network and subnetworks were subsequently carried out. Finally, the integrated miRNA–transcription factor (TF)–DEG regulatory network was analyzed. Results In total, 238 DEGs were identified, of which 162 were upregulated and 76 were downregulated. Through PPI network construction, 108 nodes and 278 gene pairs were obtained, from which chemokine (C-X-C motif) ligand 9 (CXCL9), CXCL10, protein tyrosine phosphatase, receptor type C (PTPRC), and human leukocyte antigen (HLA) were screened out as hub genes. Moreover, genes associated with the immune-related pathway and immune responses were found to be significantly enriched in the process of GDM. Finally, miRNAs and TFs that target the DEGs were predicted. Conclusions Four candidate genes (viz., CXCL9, CXCL10, PTPRC, and HLA) are closely related to GDM. miR-223-3p, miR-520, and thioredoxin-binding protein may play important roles in the pathogenesis of this disease. |
ArticleNumber | 104 |
Audience | Academic |
Author | Yu, Haifeng Wang, Yuxia Song, Xiue Liu, Fangmei |
Author_xml | – sequence: 1 givenname: Yuxia surname: Wang fullname: Wang, Yuxia organization: Department of Gynecology, Jinan Central Hospital, Jinan City, 250013, Shandong Province, China – sequence: 2 givenname: Haifeng surname: Yu fullname: Yu, Haifeng organization: Department of Obstetrics, Jinan Central Hospital, No. 105 Jiefang Road, Lixia District, Jinan City, 250013, Shandong Province, China – sequence: 3 givenname: Fangmei surname: Liu fullname: Liu, Fangmei organization: Department of Obstetrics, Jinan Central Hospital, No. 105 Jiefang Road, Lixia District, Jinan City, 250013, Shandong Province, China – sequence: 4 givenname: Xiue surname: Song fullname: Song, Xiue email: xiuesss19@163.com organization: Department of Obstetrics, Jinan Central Hospital, No. 105 Jiefang Road, Lixia District, Jinan City, 250013, Shandong Province, China. xiuesss19@163.com |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31783860$$D View this record in MEDLINE/PubMed |
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CitedBy_id | crossref_primary_10_12677_ACM_2021_119635 crossref_primary_10_1016_j_bbadis_2023_166737 crossref_primary_10_1016_j_psyneuen_2021_105435 crossref_primary_10_3389_fcell_2023_1272536 crossref_primary_10_1155_2023_6996307 crossref_primary_10_1080_14767058_2021_1875432 crossref_primary_10_1111_jdi_13828 crossref_primary_10_1016_j_placenta_2021_02_012 crossref_primary_10_1038_s41598_020_76013_5 crossref_primary_10_3390_ijms23073514 |
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Keywords | Gestational diabetes mellitus Differentially expressed genes Protein-protein interaction network Transcription factors Integrated regulatory network |
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Snippet | This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM).
The GSE70493 dataset used for... Abstract Background This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). Methods The... Background This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). Methods The GSE70493... This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). The GSE70493 dataset used for... BACKGROUNDThis study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). METHODSThe GSE70493... Abstract Background This study was aimed at screening out the potential key genes and pathways associated with gestational diabetes mellitus (GDM). Methods The... |
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SubjectTerms | Antigens Biochemistry Carrier Proteins - genetics Carrier Proteins - metabolism Chemokine CXCL10 - genetics Chemokine CXCL10 - metabolism Chemokine CXCL9 - genetics Chemokine CXCL9 - metabolism Chemokines CXCL10 protein Datasets Diabetes Diabetes mellitus Diabetes, Gestational - genetics Diabetes, Gestational - metabolism Differentially expressed genes DNA binding proteins Female Gene expression Gene Expression Profiling - methods Gene Regulatory Networks Genes Genetic aspects Genomes Gestational diabetes Gestational diabetes mellitus Histocompatibility antigen HLA HLA antigens HLA Antigens - genetics HLA Antigens - metabolism Humans Immune response Insulin Integrated regulatory network Leukocyte Common Antigens - genetics Leukocyte Common Antigens - metabolism Lymphocytes Medical research MicroRNA MicroRNAs MicroRNAs - genetics MicroRNAs - metabolism miRNA Ontology Pathogenesis Phenols (Class of compounds) Phosphatases Placenta Placenta - metabolism Pregnancy Protein binding Protein interaction Protein Interaction Maps - genetics Protein Tyrosine Phosphatases - genetics Protein Tyrosine Phosphatases - metabolism Protein-protein interaction network Protein-protein interactions Protein-tyrosine-phosphatase Proteins Thioredoxin Thioredoxins Thyroid diseases Transcription (Genetics) Transcription factors Type 2 diabetes Tyrosine |
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Title | Analysis of key genes and their functions in placental tissue of patients with gestational diabetes mellitus |
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