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Expression Pattern, Interaction Network, and Functional Analysis of the Arabidopsis Botrytis Susceptible1 Interactor
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作者 Jianzhong Huang Hongbin Zhang +4 位作者 Zhuojun Li Xiuying Guan Xiaoju Zhong Peng Jia Kai Chen 《Journal of Biomedical Science and Engineering》 2024年第10期171-178,共8页
E3 ubiquitin ligases are participated in numerous processes, regulating the response to biotic and abiotic stresses. Botrytis susceptible1 interactor (BOI) is a RING (Really Interesting New Gene)-type E3 ligase that m... E3 ubiquitin ligases are participated in numerous processes, regulating the response to biotic and abiotic stresses. Botrytis susceptible1 interactor (BOI) is a RING (Really Interesting New Gene)-type E3 ligase that mediates the ubiquitination of BOS1 (Botrytis susceptible1), a transcription factor involved in stress and pathogen responses. Although BOI is an E3 ligase, there are reports to show that BOI interacts with target proteins such as DELLAs or CONSTANS to repress gibberellin responses and flowering without the degradation of the target proteins. In this article, we utilize diversified methods to comprehensively analyze the expression pattern, interaction network and function of BOI gene. Firstly, 1800 bp upstream region of BOI gene from Arabidopsis thaliana (Arabidopsis) genome was isolated, and fused GUS reporter gene. The resulting expression cassette was introduced into wild-type Arabidopsis through Agrobacterium-mediated transformation. The result demonstrated that BOI gene was expressed predominantly in leaves, siliques, young roots, and flowering tissues, indicating that BOI gene may be involved in multiple processes in plant growth and development in Arabidopsis. Besides, eight candidate interacting proteins were obtained from the Arabidopsis cDNA library via yeast two-hybrid technology, including EXO70E2 (AT5G61010), WRKY7 (AT4G24240), WRKY11 (AT4G31550), WRKY17 (AT2G24570), UBP20 (AT4G17895), L5 (AT1G12290), SAUR9 (AT4G36110) and TCP21 (AT5G08330). Functional analysis of these candidate interacting proteins manifested that they related to multiple pathways, including biological and abiotic stress, programmed cell death, protein degradation, material metabolism and transcriptional regulation. In addition, the results of the transient assay proclaimed that BOI protein affects the protein stability of EXO70E2 and L5 through its E3 ubiquitin ligase activity. Our results provide novel clues for a better understanding of molecular mechanisms underlying BOI-mediated regulations. 展开更多
关键词 E3 Ubiquitin Ligases expression Pattern Interaction network ARABIDOPSIS
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Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis 被引量:10
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作者 Kai Shi Zhi-Tong Bing +4 位作者 Gui-Qun Cao Ling Guo Ya-Na Cao Hai-Ou Jiang Mei-Xia Zhang 《International Journal of Ophthalmology(English edition)》 SCIE CAS 2015年第2期269-274,共6页
AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression lev... AIM: To identify and understand the relationship between co-expression pattern and clinic traits in uveal melanoma, weighted gene co-expression network analysis(WGCNA) is applied to investigate the gene expression levels and patient clinic features. Uveal melanoma is the most common primary eye tumor in adults. Although many studies have identified some important genes and pathways that were relevant to progress of uveal melanoma, the relationship between co-expression and clinic traits in systems level of uveal melanoma is unclear yet. We employ WGCNA to investigate the relationship underlying molecular and phenotype in this study.METHODS: Gene expression profile of uveal melanoma and patient clinic traits were collected from the Gene Expression Omnibus(GEO) database. The gene co-expression is calculated by WGCNA that is the R package software. The package is used to analyze the correlation between pairs of expression levels of genes.The function of the genes were annotated by gene ontology(GO).RESULTS: In this study, we identified four co-expression modules significantly correlated with clinictraits. Module blue positively correlated with radiotherapy treatment. Module purple positively correlates with tumor location(sclera) and negatively correlates with patient age. Module red positively correlates with sclera and negatively correlates with thickness of tumor. Module black positively correlates with the largest tumor diameter(LTD). Additionally, we identified the hug gene(top connectivity with other genes) in each module. The hub gene RPS15 A, PTGDS, CD53 and MSI2 might play a vital role in progress of uveal melanoma.CONCLUSION: From WGCNA analysis and hub gene calculation, we identified RPS15 A, PTGDS, CD53 and MSI2 might be target or diagnosis for uveal melanoma. 展开更多
关键词 weighted gene co-expression network analysis microarray data gene ontology
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MCENet: A database for maize conditional co-expression network and network characterization collaborated with multi-dimensional omics levels 被引量:3
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作者 Tian Tian Qi You +2 位作者 Hengyu Yan Wenying Xu Zhen Su 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2018年第7期351-360,共10页
Maize (Zea mays) is the most widely grown grain crop in the world, playing important roles in agriculture and industry. However, the functions of maize genes remain largely unknown. High-quality genome- wide transcr... Maize (Zea mays) is the most widely grown grain crop in the world, playing important roles in agriculture and industry. However, the functions of maize genes remain largely unknown. High-quality genome- wide transcriptome datasets provide important biological knowledge which has been widely and suc- cessfully used in plants not only by measuring gene expression levels but also by enabling co-expression analysis for predicting gene functions and modules related to agronomic traits. Recently, thousands of maize transcriptomic data are available across different inbred lines, development stages, tissues, and treatments, or even across different tissue sections and cell lines. Here, we integrated 701 transcriptomic and 108 epigenomic data and studied the different conditional networks with multi-dimensional omics levels. We constructed a searchable, integrative, one-stop online platform, the maize conditional co- expression network (MCENet) platform. MCENet provides 10 global/conditional co-expression net- works, 5 network accessional analysis toolkits (i.e., Network Search, Network Remodel, Module Finder, Network Comparison, and Dynamic Expression View) and multiple network functional support toolkits (e.g., motif and module enrichment analysis). We hope that our database might help plant research communities to identify maize functional genes or modules that regulate important agronomic traits. 展开更多
关键词 Conditional co-expression network Module finder Transcriptomic datasets Epigenomic datasets MAIZE
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Weighted Gene Co-expression Network Analysis of Gene Modules for the Prognosis of Esophageal Cancer 被引量:2
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作者 张丛 孙茜 《Journal of Huazhong University of Science and Technology(Medical Sciences)》 SCIE CAS 2017年第3期319-325,共7页
Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict t... Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas(TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time. Furthermore, survival analysis showed that 5 out of the 12 modules were related to progression-free survival(PFS) or overall survival(OS). As the most important module, the midnight blue module with 82 genes was related to PFS, apart from the patient age, tumor grade, primary treatment success, and duration of smoking and tumor histological type. Gene ontology enrichment analysis revealed that 'glycoprotein binding' was the top enriched function of midnight blue module genes. Additionally, the blue module was the exclusive gene clusters related to OS. Platelet activating factor receptor(PTAFR) and feline Gardner-Rasheed(FGR) were the top hub genes in both modeling datasets and the STRING protein interaction database. In conclusion, our study provides novel insights into the prognosis-associated genes and screens out candidate biomarkers for esophageal cancer. 展开更多
关键词 esophageal cancer The Cancer Genome Atlas co-expression network analysis weighted gene co-expression network analysis enrichment analysis
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Identification of a TSPY co-expression network associated with DNA hypomethylation and tumor gene expression in somatic cancers 被引量:2
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作者 Tatsuo Kido Yun-Fai Chris Lau 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2016年第10期577-585,共9页
Testis specific protein Y-encoded(TSPY) is a Y-located proto-oncogene predominantly expressed in normal male germ cells and various types of germ cell tumor. Significantly, TSPY is frequently expressed in somatic ca... Testis specific protein Y-encoded(TSPY) is a Y-located proto-oncogene predominantly expressed in normal male germ cells and various types of germ cell tumor. Significantly, TSPY is frequently expressed in somatic cancers including liver cancer but not in adjacent normal tissues, suggesting that ectopic TSPY expression could be associated with oncogenesis in non-germ cell cancers. Various studies demonstrated that TSPY expression promotes growth and proliferation in cancer cells; however, its relationship to other oncogenic events in TSPY-positive cancers remains unknown. The present study seeks to correlate TSPY expression with other molecular features in clinical cancer samples, by analyses of RNA-seq transcriptome and DNA methylation data in the Cancer Genome Atlas(TCGA) database. A total of 53 genes,including oncogenic lineage protein 28 homolog B(LIN28B) gene and RNA-binding motif protein Y-linked(RBMY) gene, are identified to be consistently co-expressed with TSPY, and have been collectively designated as the TSPY co-expression network(TCN). TCN genes were simultaneously activated in subsets of liver hepatocellular carcinoma(30%) and lung adenocarcinoma(10%) regardless of pathological stage, but only minimally in other cancer types. Further analysis revealed that the DNA methylation level was globally lower in the TCN-active than TCN-silent cancers. The specific expression and methylation patterns of TCN genes suggest that they could be useful as biomarkers for the diagnosis,prognosis and clinical management of cancers, especially those for liver and lung cancers, associated with TSPY co-expression network genes. 展开更多
关键词 Co-expression network DNA methylation Gene expression signature Cancer subclassification Y chromosome genes TSPY Cancer/testis antigens
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Theory Analysis of the Handover Challenge in Express Train Access Networks (ETAN) 被引量:1
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作者 HU Guoqing HUANG Anpeng +2 位作者 HE Ruisi AI Bo CHEN Zhangyuan 《China Communications》 SCIE CSCD 2014年第7期92-98,共7页
To handle the handover challenge in Express Train Access Networks(ETAN).mobility fading effects in high speed railway environments should be addressed first.Based on the investigation of fading effects in this paper,w... To handle the handover challenge in Express Train Access Networks(ETAN).mobility fading effects in high speed railway environments should be addressed first.Based on the investigation of fading effects in this paper,we obtain two theoretical bounds:HOTiming upper bound and HO-Margin lower bound,which are helpful guidelines to study the handover challenge today and in the future.Then,we apply them to analyze performance of conventional handover technologies and our proposal in ETAN.This follow-up theory analyses and simulation experiment results demonstrate that the proposed handover solution can minimize handover time up to 4ms(which is the fastest one so far),and reduce HO-Margin to 0.16 dB at a train speed of 350km/h. 展开更多
关键词 express train access network handover (HO) high speed railways HO-timing upper bound HO-margin lower bound
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Identification of key genes underlying clinical features of hepatocellular carcinoma based on weighted gene co‑expression network analysis and bioinformatics analysis
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作者 ZHANG Kan LONG Fu‑li +3 位作者 LI Yuan SHU Fa‑ming YAO Fan WEI Ai‑Ling 《Journal of Hainan Medical University》 2023年第2期49-55,共7页
Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagno... Objective: To identify module genes that are closely related to clinical features of hepatocellular carcinoma (HCC) by weighted gene co‑expression network analysis, and to provide a reference for early clinical diagnosis and treatment. Methods: GSE84598 chip data were downloaded from the GEO database, and module genes closely related to the clinical features of HCC were extracted by comprehensive weighted gene co‑expression network analysis. Hub genes were identified through protein interaction network analysis by the maximum clique centrality (MCC) algorithm;Finally, the expression of hub genes was validated by TCGA database and the Kaplan Meier plotter online database was used to evaluate the prognostic relationship between hub genes and HCC patients. Results: By comparing the gene expression data between HCC tissue samples and normal liver tissue samples, a total of 6 262 differentially expressed genes were obtained, of which 2 207 were upregulated and 4 055 were downregulated. Weighted gene co‑expression network analysis was applied to identify 120 genes of key modules. By intersecting with the differentially expressed genes, 115 candidate hub genes were obtained. The results of enrichment analysis showed that the candidate hub genes were closely related to cell mitosis, p53 signaling pathway and so on. Further application of the MCC algorithm to the protein interaction network of 115 candidate hub genes identified five hub genes, namely NUF2, RRM2, UBE2C, CDC20 and MAD2L1. Validation of hub genes by TCGA database revealed that all five hub genes were significantly upregulated in HCC tissues compared to normal liver tissues;Moreover, survival analysis revealed that high expression of hub genes was closely associated with poor prognosis in HCC patients. Conclusions: This study identifies five hub genes by combining multiple databases, which may provide directions for the clinical diagnosis and treatment of HCC. 展开更多
关键词 Weighted gene co‑expression network analysis Bioinformatics Hepatocellular carcinoma Maximal clique centrality algorithm
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纤维肌痛综合征生物标记物的筛选及免疫细胞浸润分析 被引量:1
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作者 刘雅妮 杨静欢 +5 位作者 陆慧慧 易玉芳 李智翔 欧阳福 吴璟莉 魏兵 《中国组织工程研究》 CAS 北大核心 2025年第5期1091-1100,共10页
背景:纤维肌痛综合征作为常见风湿病,其发病与中枢敏化及免疫异常有关,但具体过程尚未阐明,缺乏特异性诊断标志物,不断探索该病的发病机制具有重要的临床意义。目的:基于加权基因共表达网络分析(WGCNA)等生物信息学方法和机器学习算法... 背景:纤维肌痛综合征作为常见风湿病,其发病与中枢敏化及免疫异常有关,但具体过程尚未阐明,缺乏特异性诊断标志物,不断探索该病的发病机制具有重要的临床意义。目的:基于加权基因共表达网络分析(WGCNA)等生物信息学方法和机器学习算法筛选纤维肌痛综合征潜在的诊断相关标志基因,并分析其免疫细胞浸润特征。方法:对来自基因表达综合数据库(GEO)的纤维肌痛综合征数据集转录谱进行差异分析和WGCNA分析,整合筛选出差异共表达基因,进一步采用机器学习套索回归(LASSO)算法、支持向量机递归特征消除(SVM-RFE)机器学习算法来识别核心生物标志物,并绘制受试者工作特征(ROC)曲线以评估诊断价值。最后,采用单样本基因集富集分析(ssGSEA)和基因集富集分析(GSEA)评估纤维肌痛综合征的免疫细胞浸润情况及通路富集。结果与结论:①对GSE67311数据集按照log2|(FC)|>0,P<0.05的条件进行差异分析后获得8个下调的差异表达基因;进行WGCNA分析后获得正相关性最高(r=0.22,P=0.04)的模块(MEdarkviolet)内含基因497个,负相关性最高(r=-0.41,P=6×10-5)的模块(MEsalmon2)内含基因19个;将差异表达基因与WGCNA的2个高相关性模块基因取交集,获得7个基因。②对上述7个基因进行LASSO回归算法筛选出4个基因,进行SVM-RFE机器学习算法筛选出5个基因,两者取交集后确定了3个核心基因,分别为重组1号染色体开放阅读框150蛋白(germinal center associated signaling and motility like,GCSAML)、整合素β8(Integrin beta-8,ITGB8)和羧肽酶A3(carboxypeptidase A3,CPA3);绘制3个核心基因的ROC曲线下面积分别为0.744,0.739,0.734,提示均具有很好的诊断价值,可作为纤维肌痛综合征的生物标志物。③免疫浸润分析结果显示,与对照组相比纤维肌痛综合征患者记忆B细胞、CD56 bright NK细胞和肥大细胞显著下调(P<0.05),且与上述3个生物标志物显著正相关(P<0.05)。④富集分析结果提示,纤维肌痛综合征的富集途径包括9条,主要与嗅觉传导、神经活性配体-受体相互作用及感染等通路密切相关。⑤上述结果显示,纤维肌痛综合征的发生发展与多基因参与、免疫调节异常及多个通路失调有关,但这些基因与免疫细胞之间的相互作用,以及它们与各通路之间的关系尚需进一步研究。 展开更多
关键词 纤维肌痛综合征 生物信息学 机器学习 免疫浸润 加权基因共表达网络分析 套索回归 支持向量机递归特征消除算法 单样本基因集富集分析 基因集富集分析
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基于WGCNA分析CPPU和TDZ对天工墨玉葡萄香气影响及关键基因挖掘
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作者 郑婷 向江 +2 位作者 魏灵珠 吴江 程建徽 《浙江农业学报》 北大核心 2025年第2期311-320,共10页
为研究处理剂对无核葡萄香气的影响,以天工墨玉为试材,用氯吡脲(CPPU)和噻苯隆(TDZ)搭配赤霉素(GA3)处理花序,检测成熟果实香气组分和萜类代谢基因表达水平,结合转录组通过加权基因共表达网络分析(WGCNA)探析萜类组分的变化,筛选相关基... 为研究处理剂对无核葡萄香气的影响,以天工墨玉为试材,用氯吡脲(CPPU)和噻苯隆(TDZ)搭配赤霉素(GA3)处理花序,检测成熟果实香气组分和萜类代谢基因表达水平,结合转录组通过加权基因共表达网络分析(WGCNA)探析萜类组分的变化,筛选相关基因。结果表明,在成熟果实中共有35种香气组分,其中,萜类13种。处理后,特征物质——橙花醇、香叶醇和芳樟醇的含量显著(P<0.05)下降。萜类合成甲羟戊酸途径(mevalonate pathway,MVA)关键基因HMGR在处理后表达降低;2-甲基赤藓糖醇-4-磷酸路径(methylerythritol phosphate pathway,MEP)关键基因DXR在CPPU处理后呈下降-上升趋势,TDZ相反。WGCNA结果显示,芳樟醇、橙花醇和香叶醇聚在一起,与turquoise模块高度相关,关联到MYB44基因在处理后大幅下调,尤其TDZ处理后,与物质含量变化一致。研究结果为葡萄生产中CPPU和TDZ的使用提供了理论依据。 展开更多
关键词 葡萄 香气 氯吡脲(CPPU) 噻苯隆(TDZ) 加权基因共表达网络分析(WGCNA)
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基于转录组分析挖掘影响甘蓝型油菜含油量积累的候选基因
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作者 李文 姚敏 +5 位作者 贺丹 邱萍 何昕 熊兴华 刘忠松 钱论文 《华北农学报》 北大核心 2025年第5期47-54,共8页
为了明晰甘蓝型油菜油脂积累的调控网络,选育高含油量油菜品种。以4个油菜自交系材料开花后25,35,45 d的种子转录组数据为样本,基于转录组和关联分析结合挖掘影响含油量的候选基因。转录组分析检测到1 530个基因在3个不同时期都存在差... 为了明晰甘蓝型油菜油脂积累的调控网络,选育高含油量油菜品种。以4个油菜自交系材料开花后25,35,45 d的种子转录组数据为样本,基于转录组和关联分析结合挖掘影响含油量的候选基因。转录组分析检测到1 530个基因在3个不同时期都存在差异表达,其中包括986个上调表达基因和544个下调表达基因。对这些差异表达基因进行GO富集分析,检测到83个油脂合成基因,79个油脂降解基因,21个油脂转运基因和80个转录因子。对差异表达转录因子进一步分析,检测到Bn TT8、Bn GL2、BnNAC082等基因。结合50份重测序甘蓝型油菜在2 a 3个不同区域的含油量表型,利用全基因组关联分析(GWAS)检测到BnNAC082-A03基因外显子区域的4个SNP与含油量显著关联,并检测到该基因区域存在2个单体型等位基因且BnNAC082-A03_Hap1对应材料的含油量显著高于BnNAC082-A03_Hap2对应材料。利用分析获得的转录组数据构建共表达网络,在子网络中检测到BnNAC082-A03与Bn TT8-A09和Bn GL2-C06直接相连,形成了影响种子油脂积累的潜在分子调控网络。 展开更多
关键词 甘蓝型油菜 含油量 转录组分析 共表达网络 全基因组关联分析
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Quantitative Expression of Heat Flow versus Tectonic Deformation in the China Continent: The Effects of Plastic-Flow Network and Stable Block 被引量:1
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作者 WANG Sheng-zu 《Acta Geologica Sinica(English Edition)》 SCIE CAS CSCD 2006年第1期97-109,共13页
Based on the heat flow data published in 1990 and 2001, a study of the factors influencing the terrestrial heat flow distribution in the China continent and its quantitative expression is carried out using the "Netli... Based on the heat flow data published in 1990 and 2001, a study of the factors influencing the terrestrial heat flow distribution in the China continent and its quantitative expression is carried out using the "Netlike Plastic-Flow" continental dynamics model and the methods of statistic analysis and optimum fitting. The result indicates that the factors influencing the heat flow distribution is classified into two groups, i.e. background and tectonic ones, in which the former mainly involves the non- uniform distribution of mantle heat flow, heat production of radioactive dements in the crust, heattransfer media and hydrothermal circulation, while the latter mainly involves plastic-flow networks and relatively-stable blocks. The plastic-flow network is a manifestation of shear localization in the netlike plastic-flow process in the lower lithosphere, which is composed of two sets of plastic-flow belts (PFBs) intersecting each other and, as one of the basic action regimes, controls the intraplate tectonic deformation. Relatively stable blocks (RSBs), which are the tectonic units with relatively-high viscosities existing in the netlike plastic-flow field, as one of the principal origins, result in the development of large-seale compressional basins. PFB and RSB, as the active and quiet states of tectonic deformation, give rise to the higher and lower heat flow values, respectivdy. The provincial average heat flow in continent can be estimated using the expression qav = q0 + a Pbt-c Pbk, where the three terms of the right side are background heat flow, PFB-positive contribution and RSB-negative contribution, Pbt and Pbk are the PFB- and RSB-coverage ratios, respectively, a is the coefficient of PFB- positive contribution depending mainly on the strain in the lower lithosphere, and c is the coefficient of RSB-negative contribution related mainly to the thickness of the lithosphere, the aseismic-area ratio and the tectonic age. For the major portion of the China continent excluding some of the southeastern region of China, the confidence interval of the provincial average background heat flow is qo=57.25±24.8 mW/m^2 and the PFB-positive- and RSB-negative-contribution coefficients are a=14.8-71.9 mW/m^2 and c=0-25.6 mW/m^2, respectively. The concepts of PFB and RSB effects and the heat flow expression suggested provide a new choice of the approach to the quantitative description of the characteristics of heat flow distribution in continent and their physical mechanisms. 展开更多
关键词 continental lithosphere terrestrial heat flow plastic-flow network relatively stable block heat-flow expression
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结合GWAS和WGCNA挖掘油菜种子次生休眠候选基因
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作者 刘福霞 刘磊 +10 位作者 白姝雯 古炫炫 吴桂琴 王旭 于文庚 李伟强 谷玉娟 孙慧 丁福全 吴德鹏 赵祥祥 《中国油料作物学报》 北大核心 2025年第3期601-615,共15页
次生休眠特性是油菜地下种子库长期存在以及自生苗繁衍的重要原因,直接影响油菜的生产安全。为定位油菜种子次生休眠的遗传位点,以106份甘蓝型油菜种质资源作为研究群体,采用油菜90 K芯片对自然群体进行基因分型,共获得29968个高质量的... 次生休眠特性是油菜地下种子库长期存在以及自生苗繁衍的重要原因,直接影响油菜的生产安全。为定位油菜种子次生休眠的遗传位点,以106份甘蓝型油菜种质资源作为研究群体,采用油菜90 K芯片对自然群体进行基因分型,共获得29968个高质量的单核苷酸多态性(SNP)标记,对3年次生休眠表型进行全基因组关联分析,最终共定位到24个与油菜次生休眠显著相关的位点。同时,基于次生休眠特性差异显著的两份材料的转录组数据,进行了加权基因共表达网络分析。结合全基因组关联分析和加权基因共表达网络分析两种策略,共鉴定到52个油菜种子次生休眠候选基因,为加速甘蓝型油菜种子次生休眠的遗传改良提供了资源。 展开更多
关键词 甘蓝型油菜 次生休眠 自然群体 全基因组关联分析 加权基因共表达网络分析
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HMM-Based Photo-Realistic Talking Face Synthesis Using Facial Expression Parameter Mapping with Deep Neural Networks
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作者 Kazuki Sato Takashi Nose Akinori Ito 《Journal of Computer and Communications》 2017年第10期50-65,共16页
This paper proposes a technique for synthesizing a pixel-based photo-realistic talking face animation using two-step synthesis with HMMs and DNNs. We introduce facial expression parameters as an intermediate represent... This paper proposes a technique for synthesizing a pixel-based photo-realistic talking face animation using two-step synthesis with HMMs and DNNs. We introduce facial expression parameters as an intermediate representation that has a good correspondence with both of the input contexts and the output pixel data of face images. The sequences of the facial expression parameters are modeled using context-dependent HMMs with static and dynamic features. The mapping from the expression parameters to the target pixel images are trained using DNNs. We examine the required amount of the training data for HMMs and DNNs and compare the performance of the proposed technique with the conventional PCA-based technique through objective and subjective evaluation experiments. 展开更多
关键词 Visual-Speech SYNTHESIS TALKING Head Hidden MARKOV Models (HMMs) Deep Neural networks (DNNs) FACIAL expression Parameter
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风险扰动视角下中欧班列运输网络韧性评估 被引量:1
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作者 冯芬玲 方源 +1 位作者 张泽 董开云 《交通运输系统工程与信息》 北大核心 2025年第2期338-351,共14页
中欧班列涉及多地区跨国运输,安全管理面临高度不确定性和复杂性。为提升中欧班列运输网络的风险防控能力,本文结合网络流理论与韧性理论,采用熵权-优劣解距离(TOPSIS)法评估节点风险,并将其融入网络加权扰动过程;引入虚拟弧表示扰动下... 中欧班列涉及多地区跨国运输,安全管理面临高度不确定性和复杂性。为提升中欧班列运输网络的风险防控能力,本文结合网络流理论与韧性理论,采用熵权-优劣解距离(TOPSIS)法评估节点风险,并将其融入网络加权扰动过程;引入虚拟弧表示扰动下的未满足运输需求,构建风险扰动下的货流分配模型;以全局网络效率为结构指标,以货流保留比为功能指标,从结构与功能双视角量化不同扰动节点与扰动规模下中欧班列运输网络的韧性表现,并提出相应的韧性优化策略。结果表明:中欧班列运输网络自身具有一定的风险化解能力,单节点发生扰动时,74.36%的节点给网络带来的结构损失小于1%,53.45%的节点功能损失小于1%,网络中的低韧性节点主要分布在西部出境通道、集结中心与新亚欧大陆桥沿线;中欧班列运输网络的功能韧性比结构韧性更容易受到风险扰动影响,且其恢复过程呈现出非线性特征;韧性提升方面,本文提出的基于风险和韧性聚类的综合保护策略可以使网络在应对大规模扰动时韧性表现同比提升38.24%,效果优于基于节点风险大小的传统节点保护策略。研究成果可为中欧班列网络韧性评估与抗风险能力提升提供参考。 展开更多
关键词 铁路运输 网络韧性 韧性三角理论 中欧班列 风险扰动 复杂网络
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基于加权基因共表达网络分析探讨急性胰腺炎相关脓毒症潜在的关键基因
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作者 桑珍珍 冯顺易 李勇 《安徽医药》 2025年第5期940-944,I0002,I0003,I0004,共8页
目的旨在识别急性胰腺炎相关脓毒症的关键基因。方法2023年3―9月从GEO数据库下载基因数据集。采用WGCNA确定急性胰腺炎和脓毒症的枢纽模块,并将两个模块交叉以确定与急性胰腺炎相关脓毒症有关的共同基因。采用R软件筛选出急性胰腺炎和... 目的旨在识别急性胰腺炎相关脓毒症的关键基因。方法2023年3―9月从GEO数据库下载基因数据集。采用WGCNA确定急性胰腺炎和脓毒症的枢纽模块,并将两个模块交叉以确定与急性胰腺炎相关脓毒症有关的共同基因。采用R软件筛选出急性胰腺炎和脓毒症的差异表达基因,同时结合WGCNA和差异分析的结果,得到与急性胰腺炎和脓毒症相关的候选基因,最后将两者取交集得到急性胰腺炎相关脓毒症的关键基因。利用GO和KEGG对急性胰腺炎和脓毒症的交集差异表达基因进行功能富集分析。结果WGCNA分析得到6个急性胰腺炎相关枢纽模块和12个脓毒症相关枢纽模块,将其交叉后共获得161个共同基因。结合WGCNA和差异分析的结果,得出与急性胰腺炎和脓毒症相关的候选基因,通过将候选基因交叉,共筛选出11个关键基因(CRISP3、ENTPD7、ERLIN1、HK3、JAK2、KLRF1、MMP9、NEU1、PLP2、SH3GLB1、TP53I3)。根据功能富集分析,急性胰腺炎相关脓毒症的关键基因主要在免疫和炎症相关通路中增强。结论CRISP3、ENTPD7、ERLIN1、HK3、JAK2、KLRF1、MMP9、NEU1、PLP2、SH3GLB1、TP53I3可能是参与急性胰腺炎相关脓毒症的关键基因。 展开更多
关键词 急性胰腺炎 脓毒症 关键基因 加权基因共表达网络分析 基因本体论
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基于生物信息学方法挖掘调控肾透明细胞癌发生的分子生物标志物
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作者 郭峰 王晨宇 +4 位作者 史振峰 赵建华 樊文龙 艾合买提·卡德尔 倪泽称 《现代泌尿外科杂志》 2025年第3期215-222,共8页
目的采用生物信息学分析筛选与肾透明细胞癌(KIRC)发生密切相关的分子生物标志物,并验证其在临床样本中的表达水平。方法从癌症基因组图谱(TCGA)数据库获取KIRCⅠ期mRNA测序数据,用主成分分析(PCA)降维处理,筛选差异表达基因(DEGs),并对... 目的采用生物信息学分析筛选与肾透明细胞癌(KIRC)发生密切相关的分子生物标志物,并验证其在临床样本中的表达水平。方法从癌症基因组图谱(TCGA)数据库获取KIRCⅠ期mRNA测序数据,用主成分分析(PCA)降维处理,筛选差异表达基因(DEGs),并对DEGs进行GO和KEGG富集分析。采用加权基因共表达网络分析(WGCNA)筛选出与KIRC显著相关的基因,构建蛋白互作(PPI)网络筛选枢纽基因。通过受试者工作特征(ROC)曲线评估枢纽基因的诊断价值,使用生存曲线图分析其预后价值,并分析枢纽基因的mRNA表达量与KIRC病理分期的相关性。纳入来自新疆维吾尔自治区人民医院的20例KIRCⅠ期患者的临床样本,采用逆转录实时定量聚合酶链式反应(RT-qPCR)、蛋白免疫印迹法、酶联免疫吸附试验(ELISA)法检测该枢纽基因在患者肾癌及癌旁组织中的表达水平。结果共筛选出8223个DEGs,其中上调基因4092个、下调基因4131个。GO分析显示DEGs与生物粘附、质膜组成部分和转运蛋白活性等相关,KEGG分析显示DEGs与细胞粘附分子、细胞因子-细胞因子受体相互作用、病毒蛋白与细胞因子和细胞因子受体的相互作用等途径相关。WGCNA分析获得了171个与KIRCⅠ期显著相关的基因,PPI网络筛选出的枢纽基因淋巴细胞胞质蛋白2(LCP2)与KIRCⅠ期的相关性显著,ROC曲线下面积为0.96,且LCP2的表达水平与患者的总体生存率呈负相关,与患者的分期、淋巴结转移有关。临床样本验证显示,KIRCⅠ期组织中LCP2的mRNA和蛋白的相对表达水平均显著高于癌旁正常组织(P<0.0001)。结论LCP2在KIRCⅠ期组织中显著上调,可作为KIRC早期诊断与治疗的潜在分子生物标志物。 展开更多
关键词 分子生物学 生物信息学 表观遗传学 差异表达基因 肾透明细胞癌 加权基因共表达网络分析 淋巴细胞胞质蛋白2
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整合分析构建基于增强子的非小细胞肺癌预后风险模型
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作者 张伟国 陆秀宏 +2 位作者 黄钢 靳明明 程云章 《中国医学物理学杂志》 2025年第1期112-121,共10页
目的:通过整合DNA甲基组数据和转录组数据构建基于增强子的非小细胞肺癌预后风险模型。方法:使用加权基因共表达网络分析(WGCNA)从甲基化差异位点的增强子中识别非小细胞肺癌相关基因。并基于转录组数据通过LASSO-Cox回归算法构建并验... 目的:通过整合DNA甲基组数据和转录组数据构建基于增强子的非小细胞肺癌预后风险模型。方法:使用加权基因共表达网络分析(WGCNA)从甲基化差异位点的增强子中识别非小细胞肺癌相关基因。并基于转录组数据通过LASSO-Cox回归算法构建并验证预后风险模型。结果:基于非小细胞肺癌的DNA甲基组数据分析获得了19784个差异甲基化位点,并对其分布模式进行了表征,其中包括6089个差异甲基化增强子位点。WGCNA从这6089个位点筛选出79个和非小细胞肺癌高度相关的增强子位点。基于转录组数据通过LASSO-Cox回归对79个增强子位点靶基因分析,构建10个基因的预后风险模型。在训练集和验证集中分析3年、5年和10年时间依赖的受试者工作特征曲线下面积(AUC)来评估预后风险模型。结果显示,训练集和验证集中的3年、5年和10年AUC均大于0.7。最后构建预测非小细胞肺癌患者3、5、10年生存情况的列线图。结论:本研究为理解增强子在非小细胞肺癌中的作用提供了新的见解,并具有通过指导个性化治疗决策来改善患者预后的潜力。 展开更多
关键词 非小细胞肺癌 增强子 甲基化 加权基因共表达网络分析 预后
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加权基因共表达网络分析结合机器学习筛选及验证骨关节炎生物标记物
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作者 张倩 黄东锋 《中国组织工程研究》 北大核心 2026年第5期1096-1105,共10页
背景:脂质代谢异常影响软骨细胞代谢,在骨关节炎的发生和进展中有着重要的作用,但目前其机制尚不明确。目的:采用加权基因共表达网络分析结合机器学习算法鉴定骨关节炎软骨细胞脂质代谢特征基因,并进行初步验证。方法:采用加权基因共表... 背景:脂质代谢异常影响软骨细胞代谢,在骨关节炎的发生和进展中有着重要的作用,但目前其机制尚不明确。目的:采用加权基因共表达网络分析结合机器学习算法鉴定骨关节炎软骨细胞脂质代谢特征基因,并进行初步验证。方法:采用加权基因共表达网络分析和微阵列数据的线性模型获得差异共表达基因,结合机器学习方法,最终筛选得到脂质代谢相关的特征基因。通过蛋白质互作网络分析,探究差异共表达基因的蛋白质互作网络关系;采用基因本体论和京都基因与基因组百科全书富集分析探索差异共表达基因所在信号通路;运用免疫相关性分析鉴定特征基因与免疫细胞浸润模式;体外分子实验验证特征基因的mRNA和蛋白表达水平。结果与结论:①经数据标准化处理和主成分分析、加权基因共表达网络分析和微阵列数据的线性模型获得高/低表达的差异共表达基因123和110个;②运用逻辑回归、随机森林和支持向量机3种机器学习算法筛选得到特征基因37个,最终得到2个脂质代谢相关的特征基因SMPD3和CYP4F3;③蛋白质互作网络分析显示SMPD3和CYP4F3蛋白相互作用均较低;④基因本体论结果显示差异共表达基因主要富集在中性粒细胞脱颗粒、中性粒细胞免疫反应和应答、中性粒细胞激活和白细胞脱颗粒等;而京都基因与基因组百科全书富集分析提示差异共表达基因主要涉及细胞外基质受体的作用和黏附等关键通路;⑤基于基因表达数据的细胞类型亚型鉴定分析显示8种免疫细胞在骨关节炎中具有显著差异;相关性分析显示SMPD3与静息态树突状细胞显著正相关(r=0.44,P=3.6×10^(-3)),与中性粒细胞显著负相关(r=-0.48,P=1.7×10^(-3));而CYP4F3与单核细胞和中性粒细胞显著正相关(r=0.76,P=7.6×10^(-9);r=0.73,P=6.0×10^(-8)),与T细胞滤泡辅助细胞和静息态树突状细胞显著负相关(r=-0.38,P=0.01;r=-0.38,P=0.01);⑥体外分子实验证明,在骨关节炎组SMPD3 mRNA和蛋白水平显著增高,而CYP4F3降低;⑦结果显示,骨关节炎软骨细胞脂质代谢特征基因SMPD3和CYP4F3可作为骨关节炎靶向治疗及软骨修复或退变的潜在生物标记物,为深入探究国人群体中脂质代谢异常与骨关节炎的关系及临床靶向治疗提供新策略。 展开更多
关键词 骨关节炎 脂质代谢 加权基因共表达网络分析 机器学习 靶向治疗 软骨修复或退变
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权重基因共表达网络分析筛选乳腺癌脑转移相关通路及预测模型构建
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作者 胡萍 朱丽佳 +2 位作者 王秋婷 谢嘉欣 林美珍 《中国优生与遗传杂志》 2025年第3期491-498,共8页
目的通过权重基因共表达网络分析(WGCNA)筛选乳腺癌脑转移(BCBM)相关通路,构建预测模型。方法从基因表达综合数据库(GEO)获取GSE125989、GSE52604数据集,基于GSE125989数据集构建WGCNA,识别与BCBM相关的关键模块并进行基因本体论(GO)、K... 目的通过权重基因共表达网络分析(WGCNA)筛选乳腺癌脑转移(BCBM)相关通路,构建预测模型。方法从基因表达综合数据库(GEO)获取GSE125989、GSE52604数据集,基于GSE125989数据集构建WGCNA,识别与BCBM相关的关键模块并进行基因本体论(GO)、KEGG分析。分析WGCNA关键模块基因与BCBM与非肿瘤性脑组织之间差异表达基因的交集,通过LASSO-Cox回归分析筛选BCBM相关基因,建立风险评分模型,根据中位风险评分将GSE125989、GSE52604数据集患者分为高、低风险组,绘制生存曲线。通过基因集富集分析(GSEA)获得高、低风险组显著富集的生物学通路。单、多因素Cox回归分析BCBM独立预测因素,建立列线图模型并进行模型评价。结果WGCNA中黄色模块(104个基因)与BCBM显著相关(r=0.63),该模块基因可能与分支上皮的形态发生、分支结构的形态发生等生物学过程和信号通路相关。经维恩图、LASSO-Cox回归分析最终获得了12个BCBM相关基因。训练集、验证集低风险组生存率均高于高风险组(P<0.05),时间依赖性ROC曲线AUC分别为0.731、0.667。风险评分、癌症分期、年龄为BCBM的独立预测因素(P<0.05),列线图预测模型预测能力较高。结论基于WGCNA关键模块筛选获得的BCBM相关基因建立的BCBM预测模型预测能力较高,探索与这些基因相关的信号通路利于预测BCBM的发生发展。 展开更多
关键词 权重基因共表达网络分析 乳腺癌 脑转移 信号通路 预测模型
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融合关键区域信息的双流网络视频表情识别
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作者 孔英会 崔文婷 +1 位作者 张珂 车辚辚 《智能系统学报》 北大核心 2025年第3期658-669,共12页
人脸表情识别是计算机视觉领域中的一个重要研究课题,而视频中的表情识别在很多场景下具有实用价值。视频序列包含丰富的帧内空间信息与帧间时间信息,同时面部关键区域的提取也对表情识别结果有重要影响,本文提出一种融合关键区域信息... 人脸表情识别是计算机视觉领域中的一个重要研究课题,而视频中的表情识别在很多场景下具有实用价值。视频序列包含丰富的帧内空间信息与帧间时间信息,同时面部关键区域的提取也对表情识别结果有重要影响,本文提出一种融合关键区域信息的双流网络表情识别方法。构建空间-时间双流网络,其中空间网络分支结合面部运动单元和CSFA(channel-spatial frame attention),重点关注影响表情识别结果的面部关键区域,以实现空间特征的有效提取;时间分支通过Farneback提取光流获得帧间的表情运动信息,并借助空间关键区域掩模选取降低光流计算复杂度。对空间-时间双流网络识别结果进行决策融合,得到最终视频表情识别结果。该方法在eNTERFACE'05、CK+数据集上进行实验测试,结果表明本文所提方法可有效提升识别精度,且提高了运行效率。 展开更多
关键词 视频表情识别 双流网络 注意力机制 光流 卷积神经网络 掩模 特征融合 面部表情识别
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