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The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes

In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. In this study, the dataset G...

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Autores principales: Jia, Keren, Wu, Yingcheng, Ju, Jingyi, Wang, Liyang, Shi, Lili, Wu, Huiqun, Jiang, Kui, Dong, Jiancheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368838/
https://www.ncbi.nlm.nih.gov/pubmed/30755828
http://dx.doi.org/10.7717/peerj.6343
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author Jia, Keren
Wu, Yingcheng
Ju, Jingyi
Wang, Liyang
Shi, Lili
Wu, Huiqun
Jiang, Kui
Dong, Jiancheng
author_facet Jia, Keren
Wu, Yingcheng
Ju, Jingyi
Wang, Liyang
Shi, Lili
Wu, Huiqun
Jiang, Kui
Dong, Jiancheng
author_sort Jia, Keren
collection PubMed
description In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. In this study, the dataset GSE9006 was downloaded from the GEO (Gene Expression Omnibus database); it includes 24 healthy children, 43 children with newly diagnosed Type 1 diabetes (T1D), and 12 children with newly diagnosed T2D. These data were used for differentially expressed genes (DGEs) analysis and weighted co-expression network analysis (WGCNA). We identified 192 up-regulated genes and 329 down-regulated genes by performing DEGs analysis. By performing WGGNA, we found that blue module (539 genes) was highly correlated to cyan module (97 genes). Gene ontology (GO) and pathway enrichment analyses were performed to figure out the functions and related pathways of genes, which were identified in the results of DEGs and WGCNA. Genes with conspicuous logFC and in the high correlated modules were input into GeneMANIA, which is a plugin of Cytoscape application. Thus, we constructed the protein-protein interaction (PPI) network (92 nodes and 254 pairs). Eventually, we analyzed the transcription factors and references related to genes with conspicuous logFC or high-degree genes, which were present in both the modules of WGCNA and PPI network. Current research shows that EGR1 and NAMPT can be used as marker genes for childhood-onset T2D. Gestational diabetes and chronic inflammation are risk factors that lead to the development of childhood-onset T2D.
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spelling pubmed-63688382019-02-12 The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes Jia, Keren Wu, Yingcheng Ju, Jingyi Wang, Liyang Shi, Lili Wu, Huiqun Jiang, Kui Dong, Jiancheng PeerJ Bioinformatics In general, type 2 diabetes (T2D) usually occurs in middle-aged and elderly people. However, the incidence of childhood-onset T2D has increased all across the globe. Therefore, it is very important to determine the molecular and genetic mechanisms of childhood-onset T2D. In this study, the dataset GSE9006 was downloaded from the GEO (Gene Expression Omnibus database); it includes 24 healthy children, 43 children with newly diagnosed Type 1 diabetes (T1D), and 12 children with newly diagnosed T2D. These data were used for differentially expressed genes (DGEs) analysis and weighted co-expression network analysis (WGCNA). We identified 192 up-regulated genes and 329 down-regulated genes by performing DEGs analysis. By performing WGGNA, we found that blue module (539 genes) was highly correlated to cyan module (97 genes). Gene ontology (GO) and pathway enrichment analyses were performed to figure out the functions and related pathways of genes, which were identified in the results of DEGs and WGCNA. Genes with conspicuous logFC and in the high correlated modules were input into GeneMANIA, which is a plugin of Cytoscape application. Thus, we constructed the protein-protein interaction (PPI) network (92 nodes and 254 pairs). Eventually, we analyzed the transcription factors and references related to genes with conspicuous logFC or high-degree genes, which were present in both the modules of WGCNA and PPI network. Current research shows that EGR1 and NAMPT can be used as marker genes for childhood-onset T2D. Gestational diabetes and chronic inflammation are risk factors that lead to the development of childhood-onset T2D. PeerJ Inc. 2019-02-06 /pmc/articles/PMC6368838/ /pubmed/30755828 http://dx.doi.org/10.7717/peerj.6343 Text en ©2019 Jia et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Bioinformatics
Jia, Keren
Wu, Yingcheng
Ju, Jingyi
Wang, Liyang
Shi, Lili
Wu, Huiqun
Jiang, Kui
Dong, Jiancheng
The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
title The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
title_full The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
title_fullStr The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
title_full_unstemmed The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
title_short The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
title_sort identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes
topic Bioinformatics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6368838/
https://www.ncbi.nlm.nih.gov/pubmed/30755828
http://dx.doi.org/10.7717/peerj.6343
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