weighted gene co‐expression network analysis

加权基因共表达网络分析
  • 文章类型: Journal Article
    Finkel-Biskis-Jinkins骨肉瘤(c-Fos;由FOS编码)在几种心血管疾病中起着重要作用,包括动脉粥样硬化和中风.然而,FOS与静脉血栓栓塞(VTE)之间的关系尚不清楚.我们在基因表达综合数据集中鉴定了差异表达基因,GSE48000,包括VTE患者和健康个体,并使用CIBERSORT和加权共表达网络分析(WGCNA)对其进行了分析。FOS和CD46表达显着下调(FOSp=2.26E-05,CD64p=8.83E-05),并与VTE中的中性粒细胞活性密切相关。我们使用GSE19151并进行PCR以确认FOS和CD46具有诊断VTE的潜力;然而,只有FOS通过PCR和ELISA在全血样品中显示差异表达。此外,我们发现调节FOS表达的hsa-miR-144在VTE中显著上调.此外,VTE患者的中性粒细胞中FOS表达显著下调(p=0.03)。对VTE患者的全血样品进行的RNA测序表明,FOS通过瘦素介导的脂肪因子信号通路在VTE中发挥了作用。我们的结果表明,FOS和相关基因或蛋白质可以优于传统的临床标志物,并且可以用作VTE的诊断生物标志物。
    The Finkel-Biskis-Jinkins Osteosarcoma (c-Fos; encoded by FOS) plays an important role in several cardiovascular diseases, including atherosclerosis and stroke. However, the relationship between FOS and venous thromboembolism (VTE) remains unknown. We identified differentially expressed genes in Gene Expression Omnibus dataset, GSE48000, comprising VTE patients and healthy individuals, and analysed them using CIBERSORT and weighted co-expression network analysis (WGCNA). FOS and CD46 expressions were significantly downregulated (FOS p = 2.26E-05, CD64 p = 8.83E-05) and strongly linked to neutrophil activity in VTE. We used GSE19151 and performed PCR to confirm that FOS and CD46 had diagnostic potential for VTE; however, only FOS showed differential expression by PCR and ELISA in whole blood samples. Moreover, we found that hsa-miR-144 which regulates FOS expression was significantly upregulated in VTE. Furthermore, FOS expression was significantly downregulated in neutrophils of VTE patients (p = 0.03). RNA sequencing performed on whole blood samples of VTE patients showed that FOS exerted its effects in VTE via the leptin-mediated adipokine signalling pathway. Our results suggest that FOS and related genes or proteins can outperform traditional clinical markers and may be used as diagnostic biomarkers for VTE.
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  • 文章类型: Journal Article
    目的:强迫症(OCD)是一种复杂的精神疾病。遗传和广泛的环境因素是强迫症的常见危险因素。目的探讨强迫症的分子机制,寻找诊断和治疗强迫症的新分子靶点。
    方法:所有数据均从公共数据集下载。基于加权基因共表达网络分析(WGCNA)鉴定关键模块和候选关键mRNA。“limma”R包用于mRNA的差异表达分析。随后,还进行了差异表达的mRNAs(DEmRNAs)的功能富集分析。此外,建立了诊断模型。最后,分析OCD中免疫细胞的浸润水平及其与多中心关键DEmRNAs的相关性。
    结果:选择绿色和红色模块作为集线器模块。根据GS>0.2和MM>0.3,总共447个mRNA被认为是候选关键mRNA。在GSE60190和GSE78104数据集中鉴定了相同方向的总共26个DEmRNA。共有26个DEmRNAs与WGCNA中的候选关键mRNA交叉,以获得10个交叉DEmRNAs(HSPB1,ITPK1,CBX7,PPP1R10,TAOK1,PISD,MKNK2、RWDD1、PPA1和RELN)。然而,只有4种DMRNAs(HSPB1、TAOK1、MKNK2和PPA1)预测相关药物。随后,接收机工作特性分析表明,该诊断模型具有较高的诊断价值。此外,六个多中心关键DMRNAs(SNRPF,SNRNP70,PRPF8,NOP56,EPRS,和CCT2)通过UpSet包进行筛选。最后,研究发现6种多中心关键DMRNAs与免疫细胞相关。
    结论:本研究获得的关键分子为进一步研究强迫症的分子机制奠定了基础。
    OBJECTIVE: Obsessive-compulsive disorder (OCD) is a complex psychiatric disorder. Genetic and broad environmental factors are common risk factors for OCD. The purpose of this study is to explore the molecular mechanism of OCD and to find new molecular targets for the diagnosis and management of OCD.
    METHODS: All data were downloaded from public dataset. Key modules and candidate key mRNAs were identified based on weighted gene co-expression network analysis (WGCNA). The \"limma\" R package was used for differential expression analysis of mRNAs. Subsequently, functional enrichment analysis of differentially expressed mRNAs (DEmRNAs) was also carried out. In addition, a diagnostic model was constructed. Finally, the infiltration level of immune cells in OCD and its correlation with multicentric key DEmRNAs were analyzed.
    RESULTS: Green and red modules were selected as the hub modules. A total of 447 mRNAs were considered candidate key mRNAs according to GS > 0.2 and MM > 0.3. A total of 26 DEmRNAs in the same direction were identified in the GSE60190 and GSE78104 datasets. A total of 26 DEmRNAs were intersected with candidate key mRNAs in WGCNA to obtain 10 intersection DEmRNAs (HSPB1, ITPK1, CBX7, PPP1R10, TAOK1, PISD, MKNK2, RWDD1, PPA1, and RELN). However, only four DEmRNAs (HSPB1, TAOK1, MKNK2, and PPA1) predicted related drugs. Subsequently, receiver operating characteristic analysis shows that the diagnostic model has high diagnostic value. Moreover, six multicentric key DEmRNAs (SNRPF, SNRNP70, PRPF8, NOP56, EPRS, and CCT2) were screened by UpSet package. Finally, six multicentric key DEmRNAs were found to be associated with immune cells.
    CONCLUSIONS: The key molecules obtained in this study lay a foundation for further research on the molecular mechanism of OCD.
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  • 文章类型: Journal Article
    确定控制疾病进展的关键途径对于准确预后和有效治疗至关重要。我们开发了一种广泛适用的新颖的系统级基因发现策略。该方法集中于组成型活性雄激素受体(AR)剪接变体驱动的途径,作为前列腺癌(PC)治疗抗性的顽固性机制的代表。我们使用加权基因共表达网络分析结合实验性AR变异转录组分析对人类前列腺样本进行了荟萃分析。鉴定了在人PC进展期间上调的AR变体驱动的基因模块。我们通过在裂殖酵母中使用高通量合成遗传阵列筛选鉴定与AR变体功能性相互作用的基因来过滤该模块。该策略鉴定了七个AR变体调节的基因,这些基因也增强了AR活性并驱动癌症进展。七个基因的表达预测大型独立PC患者队列中的无病生存率较差。对基因集相互作用成员的药理学抑制有效且协同地降低了PC细胞的增殖。这种公正和新颖的基因发现策略确定了一种临床相关的,致癌,在PC中具有强大的预后和治疗潜力的相互作用基因中心。
    Identifying critical pathways governing disease progression is essential for accurate prognosis and effective therapy. We developed a broadly applicable and novel systems-level gene discovery strategy. This approach focused on constitutively active androgen receptor (AR) splice variant-driven pathways as representative of an intractable mechanism of prostate cancer (PC) therapeutic resistance. We performed a meta-analysis of human prostate samples using weighted gene co-expression network analysis combined with experimental AR variant transcriptome analyses. An AR variant-driven gene module that is upregulated during human PC progression was identified. We filtered this module by identifying genes that functionally interacted with AR variants using a high-throughput synthetic genetic array screen in Schizosaccharomyces pombe This strategy identified seven AR variant-regulated genes that also enhance AR activity and drive cancer progression. Expression of the seven genes predicted poor disease-free survival in large independent PC patient cohorts. Pharmacologic inhibition of interacting members of the gene set potently and synergistically decreased PC cell proliferation. This unbiased and novel gene discovery strategy identified a clinically relevant, oncogenic, interacting gene hub with strong prognostic and therapeutic potential in PC.
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