Weighted Gene Correlation Network Analysis (WGCNA) Detected Loss of MAGI2 Promotes Chronic Kidney Disease (CKD) by Podocyte Damage

Zuo, Zhi; Shen, Jianxiao; Pan, Yan; Pu, Juan; Li, Yonggang; Shao, Xinghua; Wang, Wanpeng

doi:10.1159/000495205

Cited by 41 publications

(36 citation statements)

References 51 publications

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“…Only 205 genes were unclassified in any module (in grey), accounting for 10.50% of DEGs. In comparison, previous studies have reported an average gene number in each module of 216 to 336 and percentage of genes not found in any module of 5.67%-33.61% of DEGs (Liu X et al, 2017;Liu Z et al, 2018;Yang Q et al, 2018;Zuo Z et al, 2018). In conclusion, our WGCNA results were comparable.…”

Section: Discussionsupporting

confidence: 63%

Peer Review #3 of "Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA (v0.2)"

2019

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Background. Adrenocortical carcinoma (ACC) is a rare and aggressive malignant cancer in the adrenal cortex with poor prognosis. Though previous research has attempted to elucidate the progression of ACC, its molecular mechanism remains poorly understood. Methods. Gene TPM (transcripts per million) data were downloaded from the UCSC Xena database, which included ACC (The Cancer Genome Atlas (TCGA), n = 77) and normal samples (Genotype Tissue Expression (GTEx), n = 128). We used weighted gene co-expression network analysis (WGCNA) to identify gene connections. Overall survival (OS) was determined using the univariate Cox model. A protein-protein interaction (PPI) network was constructed by the Search Tool for the Retrieval of Interacting Genes (STRING). Results. To determine the critical genes involved in ACC progression, we obtained 2,953 significantly differentially expressed genes (DEGs) and nine modules. Among them, the blue module demonstrated significant correlation with the "Stage" of ACC. Enrichment analysis revealed that genes in the blue module were mainly enriched in cell division, cell cycle, and DNA replication. Combined with the PPI and co-expression networks, we identified four hub genes (i.e., TOP2A, TTK, CHEK1, and CENPA) that were highly expressed in ACC and negatively correlated with OS. Thus, these identified genes may play important roles in the progression of ACC and serve as potential biomarkers for future diagnosis.

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Section: Discussionsupporting

confidence: 63%

Peer Review #3 of "Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA (v0.2)"

2019

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“…32 Other studies also have revealed that MAGI-2 genetic mutation leads to a severe renal phenotype in mice and humans. 30,[33][34][35][36] J o u r n a l P r e -p r o o f However, an understanding of the mechanism underlying the phenotype has remained elusive. In particular, although the SD in podocytes is crucial as a kidney filtration barrier, it is unclear whether MAGI-2 interacts with the SD.…”

Section: Introductionmentioning

confidence: 99%

MAGI-2 orchestrates the localization of backbone proteins in the slit diaphragm of podocytes

Yamada

Shirata

Makino

et al. 2021

Kidney International

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This is a PDF file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. This version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. Please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

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“…21 Based on the WGCNA, the module with a high correlation with the disease progression would be screened out. 29,30 The dysregulated genes in the module are usually defined as hub genes that are involved in the pathogenesis of disease. 29,30 In the present study, the differentially expressed lncRNAs and mRNAs were divided into nine modules.…”

Section: Knockdown Of Nonratt0107882 Inhibits Neuronal Apoptosismentioning

confidence: 99%

“…29,30 The dysregulated genes in the module are usually defined as hub genes that are involved in the pathogenesis of disease. 29,30 In the present study, the differentially expressed lncRNAs and mRNAs were divided into nine modules. There was a strong correlation between SE and two modules (brown module and turquoise module).…”

Section: Knockdown Of Nonratt0107882 Inhibits Neuronal Apoptosismentioning

confidence: 99%

Expression and functional analysis of lncRNAs in the hippocampus of immature rats with status epilepticus

Gan

Huang

et al. 2019

J Cellular Molecular Medi

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Long non‐coding RNAs (lncRNAs) have been implicated in the regulation of gene expression at various levels. However, to date, the expression profile of lncRNAs in status epilepticus (SE) was unclear. In our study, the expression profile of lncRNAs was investigated by high‐throughput sequencing based on a lithium/pilocarpine‐induced SE model in immature rats. Furthermore, weighted correlation network analysis (WGCNA), gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to construct co‐expression networks and establish functions of the identified hub lncRNAs in SE. The functional role of a hub lncRNA (NONRATT010788.2) in SE was investigated in an in vitro model. Our results indicated that 7082 lncRNAs (3522 up‐regulated and 3560 down‐regulated), which are involved in cell proliferation, inflammatory responses, angiogenesis and autophagy, were dysregulated in the hippocampus of immature rats with SE. Additionally, WGCNA identified 667 up‐regulated hub lncRNAs in turquoise module that were involved in apoptosis, inflammatory responses and angiogenesis via regulation of HIF‐1, p53 and chemokine signalling pathways and via inflammatory mediator regulation of TRP channels. Knockdown of an identified hub lncRNA (NONRATT010788.2) inhibited neuronal apoptosis in vitro. Taken together, our study is the first to demonstrate the expression profile and potential function of lncRNAs in the hippocampus of immature rats with SE. The defined hub lncRNAs may participate in the pathogenesis of SE via lncRNA‐miRNA‐mRNA network.

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Weighted Gene Correlation Network Analysis (WGCNA) Detected Loss of MAGI2 Promotes Chronic Kidney Disease (CKD) by Podocyte Damage

Cited by 41 publications

References 51 publications

Peer Review #3 of "Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA (v0.2)"

Peer Review #3 of "Identification of four hub genes associated with adrenocortical carcinoma progression by WGCNA (v0.2)"

MAGI-2 orchestrates the localization of backbone proteins in the slit diaphragm of podocytes

Expression and functional analysis of lncRNAs in the hippocampus of immature rats with status epilepticus

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