Transcriptome network analysis of potential candidate genes for heart failure

Chen, J.; Wang, H.Y.; Zeng, Chu‐Mei

doi:10.4238/2013.october.18.7

Cited by 8 publications

(5 citation statements)

References 32 publications

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“…However, studies of the role of JunB in heart diseases have been limited. JunB accounts for HF originating from inflammatory cardiomyopathy as revealed in a transcriptome network analysis 31 , while morpholino-mediated JunB knockdown causes HF in zebrafish 32 . It was not clear, however, if JunB was implicated in apoptotic process.…”

Section: Discussionmentioning

confidence: 99%

MicroRNA 199a-5p induces apoptosis by targeting JunB

Yan

Yang

Meng

et al. 2018

Sci Rep

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MicroRNAs participate in a variety of physiological and pathophysiological processes in various organs including the heart. Our previous work revealed that the level of miR-199a-5p was significantly higher in failing hearts than in control hearts. However, whether it is associated with the progression of heart failure (HF) and mediates cardiomyocyte apoptosis remained unclear. In the present study, we used various biochemical and molecular biological approaches to investigate the changes in miR-199a-5p levels in failing hearts in a rat model induced by acute myocardial infarction. We found that miR-199a-5p levels in the heart increased with the progression of HF, and overexpression of miR-199a-5p significantly increased apoptosis in untreated H9C2 cells and potentiated angiotensin II-induced apoptosis. Thus, our results indicate that miR-199a-5p is involved in the progression of HF and mediates cardiomyocyte apoptosis. We also confirmed that JunB, a member of the activator protein-1 transcription factor family, is one of direct targets of miR-199a-5p via a dual-luciferase reporter assay and mutagenesis on the 3′ untranslated region of the JunB gene. Consistent with the above findings, overexpression of JunB in H9c2 cells suppressed cell apoptosis. Based on our findings, miR-199a-5p induces apoptosis by targeting JunB.

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Section: Discussionmentioning

confidence: 99%

MicroRNA 199a-5p induces apoptosis by targeting JunB

Yan

Yang

Meng

et al. 2018

Sci Rep

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“…Currently, network-based analysis has become more powerful in exploring disease mechanisms (Bradley et al, 2008). Recently, protein-protein interaction (PPI) networks, gene interaction networks, and transcriptome networks have proven to be effective in characterizing cellular processes in various diseases (Chen et al, 2013;Zhu et al, 2014;Zhang et al, 2015). PPI network analysis differs from pathway analysis in that it uses comprehensive networks to gain system-level biological meanings (Wu and Chen, 2009).…”

Section: Introductionmentioning

confidence: 99%

Identification of altered pathways in hypertrophic cardiomyopathy based on combined data of protein-protein interactions and molecular pathways

Sw¹,

Wang²,

Pan³

2016

Genet. Mol. Res.

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ABSTRACT. The purpose of our study was to identify molecular pathways altered during the pathogenesis of hypertrophic cardiomyopathy (HCM) based on data from the STRING proteinprotein interaction (PPI) database and the REACTOME pathway database. Identification of differentially expressed genes (DEGs) was carried out, followed by construction of a targeted network and selection of hub genes in this network. PPI pairs in each pathway were extracted, and altered pathways were identified when the said pathway differed from common interactions within the targeted network with a P value of less than 0.05. These altered pathways were further validated based on enrichment of hub genes in pathways within the targeted network. Through this method, we identified 1085 DEGs. The DEGs were inputted into the STRING database, and the resulting targeted network was composed of 3631 interactions. Based on the selection criteria, 30 significantly changed pathways were screened in total. Among these, the top five pathways were found to be involved in immune modulation, signal transduction, hemostasis, and G protein-coupled receptor signaling. Similarly, enrichment in hub gene interactions was also found in members within the altered pathways, including those involved in the innate immune system, the immune system, and signal transduction pathways. These altered pathways are important for understanding the underlying mechanisms of HCM, and can be used for clinical application of treatments in the future.

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“…Transcriptome sequencing of different cell lines identifies several candidate genes related to coronary artery calcification [ 31 ]. Some potential candidate genes for heart failure were also discovered by transcriptome network analysis [ 32 ]. Transcriptome network analysis is also used to find divergent cardiovascular disease pathways between animal and humans [ 33 ].…”

Section: Resultsmentioning

confidence: 99%

Metabolic Pathway Genes Associated with Susceptibility Genes to Coronary Artery Disease

Lü

Chen

2018

International Journal of Genomics

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Coronary artery disease (CAD) is one of the leading threats to global health. Previous research has proven that metabolic pathway disorders, such as high blood lipids and diabetes, are one of the risk factors that mostly cause CAD. However, the crosstalk between metabolic pathways and CAD was mostly studied on physiology processes by analyzing a single gene function. A canonical correlation analysis was used to identify the metabolic pathways, which were integrated as a unit to coexpress with CAD susceptibility genes, and to resolve additional metabolic factors that are related to CAD. Seven pathways, including citrate cycle, ubiquinone, terpenoid quinone biosynthesis, and N-glycan biosynthesis, were identified as an integrated unit coexpressed with CAD genes. These pathways could not be revealed as a coexpressed pathway through traditional methods as each single gene has weak correlation. Furthermore, sets of genes in these pathways were candidate markers for diagnosis and detection from patients' serum.

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Transcriptome network analysis of potential candidate genes for heart failure

Cited by 8 publications

References 32 publications

MicroRNA 199a-5p induces apoptosis by targeting JunB

MicroRNA 199a-5p induces apoptosis by targeting JunB

Identification of altered pathways in hypertrophic cardiomyopathy based on combined data of protein-protein interactions and molecular pathways

Metabolic Pathway Genes Associated with Susceptibility Genes to Coronary Artery Disease

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