期刊文献+
任意字段
题名或关键词
题名
关键词
摘要
作者
第一作者
机构
刊名
分类号
参考文献
作者简介
基金资助
栏目信息
共找到210篇文章
< 1 2 … 11 >
每页显示 20 50 100
已选0条
引用分析
参考文献
引证文献
 统计分析
检索结果
已选文献
显示方式：
An integrative gene regulatory network identifies transcriptional hubs governing the photosynthetic apparatus in rice 认领 引用
1
作者 Ming-Ju Lyu Faming Chen +6 位作者 Xiaoya Li Aidi Luo Qingfeng Song Yangmeihui Li Xiaoyu Tu Changsong Zou Xin-Guang Zhu 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2026年第6期1058-1073,共16页
Photosynthesis fuels crop growth and yield,yet the regulatory networks coordinating photosynthetic gene expression with carbon allocation remain incompletely understood.Here,we construct a gene regulatory network(GRN)... Photosynthesis fuels crop growth and yield,yet the regulatory networks coordinating photosynthetic gene expression with carbon allocation remain incompletely understood.Here,we construct a gene regulatory network(GRN)for rice photosynthesis by integrating time-resolved RNA-seq,ATAC-seq,and promoter cis-element analyses.We identify nine hub transcription factors(TFs),four of which(OsPIL13,OsbZIP72,OsCGA1,and OsGLK1)exhibit strong leaf-specific,light-inducible expression patterns.Overexpression of OsPIL13,OsbZIP72,or OsGLK1 using photosynthetic tissue-specific promoters significantly enhanced the light-saturated photosynthetic rate(Asat)across developmental stages,with OsPIL13 overexpression increasing Asat by up to 57%during grain filling.While several hub TFs boosted photosynthetic capacity,consistent improvements in biomass and grain yield under field conditions were rare.Notably,OsGLK1 overexpression confers stable yield gains across multiple growing seasons.Comparative transcriptomic analysis indicates that OsGLK1 also upregulates genes involved in brassinosteroid biosynthesis and sugar and lipid transporter genes,potentially linking photosynthetic output to growth and resource allocation.Collectively,our findings indicate that enhancing photosynthesis alone is insufficient to guarantee yield improvement;rather,the coordinated regulation of photosynthetic capacity and downstream carbon utilization is essential for sustainable productivity gains in rice. 展开更多
关键词 Rice Photosynthesis Gene regulatory network Transcription factors Biomass Yield
暂未订购 下载PDF
Comprehensive multi-omics reveals dynamic chromatin changes and gene regulatory networks during duck folliculogenesis 认领 引用
2
作者 Zhen Li Yunxiao Sun +3 位作者 Dandan Sun Ning Yang Zhongtao Yin Zhuocheng Hou 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2026年第4期1992-2010,共19页
Background Follicular development is a prerequisite for vertebrate reproduction,and it is precisely regulated by complex genomic conformations and regulatory elements.However,the dynamic changes in the interaction bet... Background Follicular development is a prerequisite for vertebrate reproduction,and it is precisely regulated by complex genomic conformations and regulatory elements.However,the dynamic changes in the interaction between the three-dimensional genome and regulatory elements of granulosa cells(GCs)during avian follicular development are still unclear.Here,we integrated RNA sequencing,ATAC sequencing,CUT&Tag,and Hi-C of GCs in 7stages of Pekin ducks(Anas platyrhynchos domestica)to construct a high-resolution three-dimensional cis-regulatory map of follicular development,revealing the chromatin dynamics basis of avian folliculogenesis.Results Our integrative analysis reveals that H3K27ac dynamics,rather than chromatin accessibility alone,are strongly associated with the stage-specific transcriptional increase of follicle selection and maturation.We identified enhancers and super-enhancers(SEs)that are significantly correlated with the expression of key follicular genes.Regarding 3D genome organization,we observed that topologically associating domains(TADs)remained largely stable,serving as a structural scaffold.However,stage-specific boundary changes coincided with the transcriptional alterations of key regulator genes.Furthermore,we inferred putative gene regulatory networks(GRNs)comprising 46core transcription factors(TFs)predicted to be closely linked to follicular development.Finally,comparative analysis highlighted both the conservation and species-specificity of these regulatory elements between birds and mammals.Conclusions Our study provides an integrative,multi-omics resource that offers novel insights into the epigenomic landscape of duck follicular development.The resulting dataset and regulatory map establish a valuable foundation for further mechanistic studies of folliculogenesis and for understanding regulatory divergence across species. 展开更多
关键词 Bird Cis-regulatory map Folliculogenesis Regulatory network Three-dimensional
暂未订购 下载PDF
Multiscale regulatory network underlying cold exposure-induced adipose tissue remodeling:Microscopic and macroscopic perspectives 认领 引用
3
作者 Yusha Yang Guanyu Zhang +1 位作者 Xi Li Danfeng Yang 《Frigid Zone Medicine》 2026年第1期56-64,共9页
Cold exposure,a prototypical environmental stressor,activates the metabolic plasticity of adipose tissue(AT)by inducing extensive AT remodeling.This adaptive process not only enhances cold tolerance but also criticall... Cold exposure,a prototypical environmental stressor,activates the metabolic plasticity of adipose tissue(AT)by inducing extensive AT remodeling.This adaptive process not only enhances cold tolerance but also critically improves glucose and lipid(glucolipid)metabolic homeostasis through systemic metabolic reprogramming.This review synthesizes recent high-resolution sequencing studies to comprehensively examine three core dimensions of cold exposure-induced AT remodeling:tissue phenotype,cellular architecture,and metabolic function.In addition,it elucidates intercellular communication and inter-organ interactions within the multiscale regulatory networks that govern AT remodeling,thereby providing a theoretical framework for the development of intervention strategies for metabolic diseases based on mechanisms of cold-induced AT remodeling. 展开更多
关键词 cold exposure adipose tissue plasticity metabolic reprogramming intercellular communication inter-organ regulatory networks
暂未订购 下载PDF
Inference of Gene Regulatory Networks for Breast Cancer Based on Genetic Modules 认领 引用
4
作者 Yihao Chen Ling Guo +2 位作者 Yue Pan Hui Cai Zhitong Bing 《Biomedical Engineering Frontiers》 EI CAS 2025年第1期156-174,共19页
Objective:Breast cancer is a common tumor and has a high mortality rate.Gene regulatory networks(GRNs)can genetically facilitate targeted therapies for this disease.Impact Statement:This study proposes a new method to... Objective:Breast cancer is a common tumor and has a high mortality rate.Gene regulatory networks(GRNs)can genetically facilitate targeted therapies for this disease.Impact Statement:This study proposes a new method to infer GRNs.This new method combining genetic modules and convolutional neural networks is presented to infer GRNs from the RNA sequencing data of breast cancer.Introduction:GRNs play an essential role in many disease treatments.Previous studies showed that GRNs will accelerate tumor therapy.However,most of the existing network inference methods are based on large-scale gene collections,which ignore the characteristics of different tumors.Methods:In this work,weighted gene coexpression network analysis was deployed to screen key genes and gene modules.The gene regulatory associations in gene modules were then transformed into 2-dimensional histogram types.A convolutional neural network was chosen as the main framework to fit the gene regulatory types and infer the GRN.Results:The method integrates genetic data analysis and deep learning perspectives to screen key genes and predict GRNs among key genes.The key genes screened were validated by multiple methods,and the inferred gene regulatory associations were widely validated in real datasets.Conclusion:The method can be used as an auxiliary tool with the potential to predict key genes and the GRNs of key genes.It has the potential to facilitate the therapeutic process and targeted therapy for breast cancer. 展开更多
关键词 breast cancer genetic modules infer grns gene regulatory networks regulatory networks grns can convolutional neural networks rna sequencing data accelerate tumor therapyhowe
暂未订购 下载PDF
Gene regulatory network prediction using machine learning,deep learning,and hybrid approaches 认领 引用
5
作者 Sai Teja Mummadi Md Khairul Islam +1 位作者 Victor Busov Hairong Wei 《Forestry Research》 2025年第1期194-207,共14页
Construction of gene regulatory networks(GRNs)is essential for elucidating the regulatory mechanisms underlying metabolic pathways,biological processes,and complex traits.In this study,we developed and evaluated machi... Construction of gene regulatory networks(GRNs)is essential for elucidating the regulatory mechanisms underlying metabolic pathways,biological processes,and complex traits.In this study,we developed and evaluated machine learning,deep learning,and hybrid approaches for constructing GRNs by integrating prior knowledge and large-scale transcriptomic data from Arabidopsis thaliana,poplar,and maize.Among these,hybrid models that combined convolutional neural networks and machine learning consistently outperformed traditional machine learning and statistical methods,achieving over 95%accuracy on the holdout test datasets.These models not only identified a greater number of known transcription factors regulating the lignin biosynthesis pathway but also demonstrated higher precision in ranking key master regulators such as MYB46 and MYB83,as well as many upstream regulators,including members of the VND,NST,and SND families,at the top of candidate lists.To address the challenge of limited training data in non-model species,we implemented transfer learning,enabling cross-species GRN inference by applying models trained on well-characterized and data-rich species to another species with limited data.This strategy enhanced model performance and demonstrated the feasibility of knowledge transfer across species.Overall,our findings underscore the effectiveness of hybrid and transfer learning approaches in GRN prediction,offering a scalable framework for elucidating regulatory mechanisms in both model and non-model plant systems. 展开更多
关键词 elucidating regulatory mechanisms machine learningdeep learningand gene regulatory networks grns prior knowledge hybrid approaches convolutional neural networks machine learning gene regulatory network
暂未订购 下载PDF
Evolution of terpene synthases in the sesquiterpene biosynthesis pathway and analysis of their transcriptional regulatory network in Asteraceae 认领 引用
6
作者 Xiuping Yang Fanbo Meng +3 位作者 Qian Cheng Pengmian Feng Xiaoming Song Wei Chen 《Horticulture Research》 SCIE CSCD 2025年第12期120-132,共13页
The Asteraceae family,one of the largest angiosperm families,is rich in terpenoid secondary metabolites with significant medicinal value.Asteraceae plants have evolved a diverse array of terpenoid biosynthesis pathway... The Asteraceae family,one of the largest angiosperm families,is rich in terpenoid secondary metabolites with significant medicinal value.Asteraceae plants have evolved a diverse array of terpenoid biosynthesis pathways,reflecting their adaptive significance and complex regulatory mechanisms.However,the evolutionary patterns and transcriptional regulatory mechanisms governing these biosynthetic processes remain unclear.This study investigates the evolution and transcriptional regulation of terpenoid biosynthesis genes in Asteraceae.Comparative genomic analysis of 19 Asteraceae and six out-group species revealed that Asteraceae species diverged~74.03 million years ago and were distinctly divided into three subfamilies.A total of 1714 terpene synthase(TPS)genes were identified,predominantly in the TPS-a and TPS-b subfamilies.Caryophyllene-type sesquiterpene biosynthetic gene clusters(BGCs)were detected in 10 species,with their formation due to whole-genome duplication(WGD)and tandem duplication.By integrating weighted gene coexpression network analysis(WGCNA)and machine learning methods,key transcription factors regulating caryophyllene synthase(CPS)in Carthamus tinctorius were identified.A multilayered gene regulatory network was constructed to identify potential regulatory factors involved in TPS gene regulation under light stress.By exploring the evolutionary patterns and potential regulatory relationships involved in terpenoid biosynthesis in Asteraceae,this study provides important insights into TPS gene evolution.In addition,the findings also offer guidance for optimizing genetic engineering strategies in terpenoid-based drug development. 展开更多
关键词 biosynthetic processes transcriptional regulatory network evolution transcriptional regulation transcriptional regulatory mechanisms terpenoid secondary metabolites terpenoid biosynthes sesquiterpene biosynthesis terpenoid biosynthesis
暂未订购 下载PDF
Integrated analysis and systematic characterization of the regulatory network for human germline development 认领 引用
7
作者 Yashi Gu Jiayao Chen +16 位作者 Ziqi Wang Qizhe Shao Zhekai Li Yaxuan Ye Xia Xiao Yitian Xiao Wenyang Liu Sisi Xie Lingling Tong Jin Jiang Xiaoying Xiao Ya Yu Min Jin Yanxing Wei Robert S.Young Lei Hou Di Chen 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2025年第2期204-219,共16页
Primordial germ cells(PGCs)are the precursors of germline that are specified at the embryonic stage.Recent studies reveal that humans employ different mechanisms for PGC specification compared with model organisms suc... Primordial germ cells(PGCs)are the precursors of germline that are specified at the embryonic stage.Recent studies reveal that humans employ different mechanisms for PGC specification compared with model organisms such as mice.Moreover,the specific regulatory machinery remains largely unexplored,mainly due to the inaccessible nature of this complex biological process in humans.Here,we curate and integrate multi-omics data,including 581 RNA-seq,54 ATAC-seq,45 ChIP-seq,and 69 single-cell RNA-seq samples from different stages of human PGC development to recapitulate the precisely controlled and stepwise process,presenting an atlas in the human PGC database(hPGCdb).With these uniformly processed data and integrated analyses,we characterize the potential key transcription factors and regulatory networks governing human germ cell fate.We validate the important roles of some of the key factors in germ cell development by CRISPRi knockdown.We also identify the soma-germline interaction network and discover the involvement of SDC2 and LAMA4 for PGC development,as well as soma-derived NOTCH2 signaling for germ cell differentiation.Taken together,we have built a database for human PGCs(http://gffzz392dffb99feb4edfh956uoc5vxfnn6opo.ffgz.tsg.suse.edu.cn)and demonstrate that hPGCdb enables the identification of the missing pieces of mechanisms governing germline development,including both intrinsic and extrinsic regulatory programs. 展开更多
关键词 Primordial germ cells Regulatory network Soma-germ cell interaction Database
暂未订购 下载PDF
Identification of target gene-microribonucleic acid-transcription factor regulatory networks in colorectal adenoma-carcinoma sequence 认领 引用
8
作者 Junxing Li Xinmei Yan +6 位作者 Huyu Jiao Jingjing Chen Yi Lin Minghui Zhou Fuchang Jin Qiuxian Xu Zhengang Zhang 《Oncology and Translational Medicine》 CAS CSCD 2025年第3期118-137,共20页
Background:Many studies have examined the role of genes,proteins,andmicroribonucleic acids(miRNAs)in colorectal cancer(CRC).However,these studies did not establish the regulatory relationships among multi-omics,and on... Background:Many studies have examined the role of genes,proteins,andmicroribonucleic acids(miRNAs)in colorectal cancer(CRC).However,these studies did not establish the regulatory relationships among multi-omics,and only a few have investigated the key genes involved in the transition from colorectal adenoma to CRC.In this study,we established regulatory networks of target gene-miRNA-transcription factors(TFs)to elucidate the pathogenesis of CRC.Methods:Data from 70 patients with CRC were obtained from the Gene Expression Omnibus database.Bioinformatics analyses were used to identify the hub genes involved in the colorectal adenoma-carcinoma sequence.We conducted prognostic evaluations,analyzed gene co-expression patterns,assessed immune cell infiltration,and performed Mendelian randomization.A gene-miRNA-TF network was constructed and further analyzed.Results:Periostin(POSTN),thrombospondin 2(THBS2),collagen alpha-2 type I(COL1A2),and other molecules were found to interact and play key roles in the colorectal adenoma-carcinoma sequence.The 3 genes-11 miRNAs-6 TFs regulatory network we constructed was involved in this process through various pathways and interactions with immune cells.Several molecules in this network affected the final prognosis of patients with CRC.THBS2 showed a causal genetic relationship with neutrophils(p=0.035,odds ratio=1.020[95% confidence interval=1.001-1.039]).Therefore,bleomycin and other drugs may potentially improve the prognosis of patients with CRC.Conclusions:The 3 genes-11 miRNAs-6 TFs regulatory network may provide valuable insights into the pathogenesis of CRC.Additionally,some of these molecules may affect patient prognosis,serving as biomarkers or therapeutic targets.THBS2 may promote neutrophil infiltration into CRC tissues by increasing neutrophil levels in the blood. 展开更多
关键词 Regulatory networks Colorectal cancer microRNA Transcription factors Mendelian randomization
暂未订购 下载PDF
Hierarchical transcription factor and regulatory network for drought response in Betula platyphylla 认领 引用 被引量：6
9
作者 Yaqi Jia Yani Niu +5 位作者 Huimin Zhao Zhibo Wang Caiqiu Gao Chao Wang Su Chen Yucheng Wang 《Horticulture Research》 SCIE CSCD 2022年第1期13-26,共14页
Although many genes and biological processes involved in abiotic stress responses have been identified,how they are regulated remains largely unclear.Here,to study the regulatory mechanism of birch(Betula platyphylla)... Although many genes and biological processes involved in abiotic stress responses have been identified,how they are regulated remains largely unclear.Here,to study the regulatory mechanism of birch(Betula platyphylla)responding to drought induced by polyethylene glycol 6000(20%,w/v),a partial correlation coefficient-based algorithm for constructing a gene regulatory network(GRN)was proposed,and a three-layer hierarchical GRN was constructed,including 68 transcription factors and 252 structural genes.A total of 1448 predicted regulatory relationships are included,and most of them are novel.The reliability of the GRN was verified by chromatin immunoprecipitation(ChIP)-PCR and qRT-PCR based on transient transformation.About 55% of genes in the bottom layer of the GRN could confer drought tolerance.We selected two TFs,BpMADS11 and BpNAC090,fromthe top layer and characterized their function in drought tolerance.Overexpression of BpMADS11 and BpNAC090 reduces electrolyte leakage,reactive oxygen species(ROS)and malondialdehyde(MDA)contents,giving greater drought tolerance than wild-type birch.According to this GRN,the important biological processes involved in drought were identified,including‘signaling hormone pathways’,‘water transport’,‘regulation of stomatal movement’,and‘response to oxidative stress’.This work indicated that BpERF017,BpAGL61,and BpNAC090 are the key upstream regulators of birch drought tolerance.Our data clearly revealed that upstream regulators and transcription factor-DNA interaction regulate different biological processes to adapt to drought stress. 展开更多
关键词 transcription factors polyethylene glycol regulatory mechanism gene regulatory network grn regulatory network drought response hierarchical transcription factor abiotic stress responses
暂未订购 下载PDF
Deciphering the intricate hierarchical gene regulatory network:unraveling multi-level regulation and modifications driving secondary cell wall formation 认领 引用 被引量：5
10
作者 Zhigang Wei Hairong Wei 《Horticulture Research》 SCIE CSCD 2024年第2期344-366,共23页
Wood quality is predominantly determined by the amount and the composition of secondary cell walls(SCWs).Consequently,unraveling the molecular regulatory mechanisms governing SCW formation is of paramount importance f... Wood quality is predominantly determined by the amount and the composition of secondary cell walls(SCWs).Consequently,unraveling the molecular regulatory mechanisms governing SCW formation is of paramount importance for genetic engineering aimed at enhancing wood properties.Although SCW formation is known to be governed by a hierarchical gene regulatory network(HGRN),our understanding of how a HGRN operates and regulates the formation of heterogeneous SCWs for plant development and adaption to ever-changing environment remains limited.In this review,we examined the HGRNs governing SCW formation and highlighted the significant key differences between herbaceous Arabidopsis and woody plant poplar.We clarified many confusions in existing literatures regarding the HGRNs and their orthologous gene names and functions.Additionally,we revealed many network motifs including feed-forward loops,feed-back loops,and negative and positive autoregulation in the HGRNs.We also conducted a thorough review of post-transcriptional and post-translational aspects,protein-protein interactions,and epigenetic modifications of the HGRNs.Furthermore,we summarized how the HGRNs respond to environmental factors and cues,influencing SCW biosynthesis through regulatory cascades,including many regulatory chains,wiring regulations,and network motifs.Finally,we highlighted the future research directions for gaining a further understanding of molecular regulatory mechanisms underlying SCW formation. 展开更多
关键词 plant development hierarchical gene regulatory network secondary cell wall formation hierarchical gene regulatory network hgrn our wood quality secondary cell walls scws consequentlyunraveling molecular regulatory mechanisms herbaceous Arabidopsis genetic engineering
暂未订购 下载PDF
Structure and Dynamics of Artificial Regulatory Networks Evolved by Segmental Duplication and Divergence Model 认领 引用 被引量：1
11
作者 Xiang-Hong Lin Tian-Wen Zhang 《International Journal of Automation and computing》 2010年第1期105-114,共10页
Based on a model of network encoding and dynamics called the artificial genome, we propose a segmental duplication and divergence model for evolving artificial regulatory networks. We find that this class of networks ... Based on a model of network encoding and dynamics called the artificial genome, we propose a segmental duplication and divergence model for evolving artificial regulatory networks. We find that this class of networks share structural properties with natural transcriptional regulatory networks. Specifically, these networks can display scale-free and small-world structures. We also find that these networks have a higher probability to operate in the ordered regimen, and a lower probability to operate in the chaotic regimen. That is, the dynamics of these networks is similar to that of natural networks. The results show that the structure and dynamics inherent in natural networks may be in part due to their method of generation rather than being exclusively shaped by subsequent evolution under natural selection. 展开更多
关键词 Genetic regulatory network （GRN） artificial regulatory network （ARN） segmental duplication and divergence scale-free small-world largest Lyapunov exponent.
暂未订购 下载PDF
Reconstructing gene regulatory networks in single-cell transcriptomic data analysis 认领 引用 被引量：7
12
作者 Hao Dai Qi-Qi Jin +1 位作者 Lin Li Luo-Nan Chen 《Zoological Research》 SCIE CSCD 2020年第6期599-604,共6页
Gene regulatory networks play pivotal roles in our understanding of biological processes/mechanisms at the molecular level.Many studies have developed sample-specific or cell-type-specific gene regulatory networks fro... Gene regulatory networks play pivotal roles in our understanding of biological processes/mechanisms at the molecular level.Many studies have developed sample-specific or cell-type-specific gene regulatory networks from single-cell transcriptomic data based on a large amount of cell samples.Here,we review the state-of-the-art computational algorithms and describe various applications of gene regulatory networks in biological studies. 展开更多
关键词 Gene regulatory network Single-cell RNA sequencing Computational algorithm Sample-specificnetwork Cell-type-specific network Cell-specific network
暂未订购 下载PDF
Single-cell RNA-Seq reveals transcriptional regulatory networks directing the development of mouse maxillary prominence 认领 引用 被引量：3
13
作者 Jian Sun Yijun Lin +4 位作者 Nayoung Ha Jianfei Zhang Weiqi Wang Xudong Wang Qian Bian 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2023年第9期676-687,共12页
During vertebrate embryonic development,neural crest-derived ectomesenchyme within the maxillary prominences undergoes precisely coordinated proliferation and differentiation to give rise to diverse craniofacial struc... During vertebrate embryonic development,neural crest-derived ectomesenchyme within the maxillary prominences undergoes precisely coordinated proliferation and differentiation to give rise to diverse craniofacial structures,such as tooth and palate.However,the transcriptional regulatory networks underpinning such an intricate process have not been fully elucidated.Here,we perform single-cell RNA-Seq to comprehensively characterize the transcriptional dynamics during mouse maxillary development from embryonic day(E)10.5eE14.5.Our single-cell transcriptome atlas of~28,000 cells uncovers mesenchymal cell populations representing distinct differentiating states and reveals their developmental trajectory,suggesting that the segregation of dental from the palatal mesenchyme occurs at E11.5.Moreover,we identify a series of key transcription factors(TFs)associated with mesenchymal fate transitions and deduce the gene regulatory networks directed by these TFs.Collectively,our study provides important resources and insights for achieving a systems-level understanding of craniofacial morphogenesis and abnormality. 展开更多
关键词 Craniofacial development Single-cell RNA-Seq Maxillary prominences Gene regulatory network Transcription factor
暂未订购 下载PDF
Evolutionary pattern of the regulatory network for flower development:Insights gained from a comparison of two Arabidopsis species 认领 引用 被引量：3
14
作者 yang LIU Chun-Ce GUO +2 位作者 Gui-Xia XU Hong-Yan SHAN Hong-Zhi KONG 《Journal of Systematics and Evolution》 SCIE CAS CSCD 北大核心 2011年第6期528-538,共11页
Previous studies on Arabidopsis thaliana and other model plants have indicated that the development of a flower is controlled by a regulatory network composed of genes and the interactions among them. Studies on the e... Previous studies on Arabidopsis thaliana and other model plants have indicated that the development of a flower is controlled by a regulatory network composed of genes and the interactions among them. Studies on the evolution of this network will therefore help understand the genetic basis that underlies flower evolution. In this study, by reviewing the most recent published work, we added 31 genes into the previously proposed regulatory network for flower development. Thus, the number of genes reached 60. We then compared the composition, structure, and evolutionary rate of these genes between A. thaliana and one of its allies, A. lyrata. We found that two genes （FLC and MAF2） show 1 ： 2 and 2 ： 2 relationships between the two species, suggesting that they have experienced independent, post-speciation duplications. Of the remaining 58 genes, 35 （60.3%） have diverged in exon-intron structure and, consequently, code for proteins with different sequence features and functions. Molecular evolutionary analyses further revealed that, although most floral genes have evolved under strong purifying selection, some have evolved under relaxed or changed constraints, as evidenced by the elevation of nonsynonymous substitution rates and/or the presence of positively selected sites. Taken together, these results suggest that the regulatory network for flower development has evolved rather rapidly, with changes in the composition, structure, and functional constraint of genes, as well as the interactions among them, being the most important contributors. 展开更多
关键词 Arabidopsis evolution flower development regulatory network.
Reconstruction of Gene Regulatory Networks Based on Two-Stage Bayesian Network Structure Learning Algorithm 认领 引用 被引量：4
15
作者 Gui-xia Liu Wei Feng +2 位作者 Han Wang Lei Liu Chun-guang Zhou 《Journal of Bionic Engineering》 SCIE EI 2009年第1期86-92,共7页
In the post-genomic biology era,the reconstruction of gene regulatory networks from microarray gene expression data is very important to understand the underlying biological system,and it has been a challenging task i... In the post-genomic biology era,the reconstruction of gene regulatory networks from microarray gene expression data is very important to understand the underlying biological system,and it has been a challenging task in bioinformatics.The Bayesian network model has been used in reconstructing the gene regulatory network for its advantages,but how to determine the network structure and parameters is still important to be explored.This paper proposes a two-stage structure learning algorithm which integrates immune evolution algorithm to build a Bayesian network.The new algorithm is evaluated with the use of both simulated and yeast cell cycle data.The experimental results indicate that the proposed algorithm can find many of the known real regulatory relationships from literature and predict the others unknown with high validity and accuracy. 展开更多
关键词 gene regulatory networks two-stage learning algorithm Bayesian network immune evolutionary algorithm
Small but influential:the role of microRNAs on gene regulatory network and 3′UTR evolution 认领 引用 被引量：16
16
作者 Rui Zhang Bing Su 《Journal of Genetics and Genomics》 SCIE CAS 2009年第1期1-6,共6页
MicroRNAs （miRNAs） are endogenous -22 nucleotide noncoding RNAs that regulate the expression of complementary messenger RNAs （mRNAs）. Thousands of miRNA genes have been found in diverse species, and many of them a... MicroRNAs （miRNAs） are endogenous -22 nucleotide noncoding RNAs that regulate the expression of complementary messenger RNAs （mRNAs）. Thousands of miRNA genes have been found in diverse species, and many of them are highly conserved. With the miRNA roles identified in nearly all aspects of biological processes, evidence is mounting that miRNAs could represent a new layer of regulatory network, and their regulatory effect might be much more pervasive than previously suspected. Here we focus on the posttranscriptional level gene regulation of miRNAs in animals and review how the miRNAs act to sustain and shape up the expression profiles of specific cell types; how the miRNAs integrate into the existing gene regulatory networks; and how the miRNAs influence the evolution of 3＇UTR of mammalian mRNAs. 展开更多
关键词 miRNA gene expression regulatory network 3＇UTR evolution
暂未订购 下载PDF
Construction of the underlying circRNA-miRNA-mRNA regulatory network and a new diagnostic model in ulcerative colitis by bioinformatics analysis 认领 引用 被引量：2
17
作者 Yu-Yi Yuan Hui Wu +2 位作者 Qian-Yun Chen Heng Fan Bo Shuai 《World Journal of Clinical Cases》 SCIE 2024年第9期1606-1621,共16页
BACKGROUND Circular RNAs(circRNAs)are involved in the pathogenesis of many diseases through competing endogenous RNA(ceRNA)regulatory mechanisms.AIM To investigate a circRNA-related ceRNA regulatory network and a new ... BACKGROUND Circular RNAs(circRNAs)are involved in the pathogenesis of many diseases through competing endogenous RNA(ceRNA)regulatory mechanisms.AIM To investigate a circRNA-related ceRNA regulatory network and a new predictive model by circRNA to understand the diagnostic mechanism of circRNAs in ulcerative colitis(UC).METHODS We obtained gene expression profiles of circRNAs,miRNAs,and mRNAs in UC from the Gene Expression Omnibus dataset.The circRNA-miRNA-mRNA network was constructed based on circRNA-miRNA and miRNA-mRNA interactions.Functional enrichment analysis was performed to identify the biological mechanisms involved in circRNAs.We identified the most relevant differential circRNAs for diagnosing UC and constructed a new predictive nomogram,whose efficacy was tested with the C-index,receiver operating characteristic curve(ROC),and decision curve analysis(DCA).RESULTS A circRNA-miRNA-mRNA regulatory network was obtained,containing 12 circRNAs,three miRNAs,and 38 mRNAs.Two optimal prognostic-related differentially expressed circRNAs,hsa_circ_0085323 and hsa_circ_0036906,were included to construct a predictive nomogram.The model showed good discrimination,with a C-index of 1(>0.9,high accuracy).ROC and DCA suggested that the nomogram had a beneficial diagnostic ability.CONCLUSION This novel predictive nomogram incorporating hsa_circ_0085323 and hsa_circ_0036906 can be conveniently used to predict the risk of UC.The circRNa-miRNA-mRNA network in UC could be more clinically significant. 展开更多
关键词 Circular RNAs RNA regulatory network Ulcerative colitis New predictive model Bioinformatics Diagnose
暂未订购 下载PDF
Molecular Regulatory Network of Flowering by Photoperiod and Temperature in Rice 认领 引用 被引量：4
18
作者 SONG Yuan-li LUAN Wei-jiang 《Rice science》 2012年第3期169-176,共8页
Plants have an ability to flower under optimal seasonal conditions to ensure reproductive success.Photoperiod and temperature are two important season-dependent factors of plant flowering.The floral transition of plan... Plants have an ability to flower under optimal seasonal conditions to ensure reproductive success.Photoperiod and temperature are two important season-dependent factors of plant flowering.The floral transition of plants depends on accurate measurement of changes in photoperiod and temperature.Recent advances in molecular biology and genetics on Arabidopsis and rice reveals that the regulation of plant flowering by photoperiod and temperature are involved in a complicated gene network with different regulatory pathways,and new evidence and understanding were provided in the regulation of rice flowering.Here,we summarize and analyze different flowering regulatory pathways in detail in rice based on previous studies and our results,including short-day promotion,long-day suppression,long-day induction of flowering,night break,different light-quality and temperature regulation pathways. 展开更多
关键词 rice flowering photoperiod temperature regulatory network
暂未订购 下载PDF
De novo gene integration into regulatory networks via interaction with conserved genes in peach 认领 引用 被引量：1
19
作者 Yunpeng Cao Jiayi Hong +7 位作者 Yun Zhao Xiaoxu Li Xiaofeng Feng Han Wang Lin Zhang Mengfei Lin Yongping Cai Yuepeng Han 《Horticulture Research》 SCIE CSCD 2024年第12期39-50,共12页
De novo genes can evolve“from scratch”from noncoding sequences,acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits... De novo genes can evolve“from scratch”from noncoding sequences,acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits.However,identifying de novo genes is challenging,as it requires high-quality genomes from closely related species.According to the comparison with nine closely related Prunus genomes,we determined at least 178 de novo genes in P.persica“baifeng”.The distinct differences were observed between de novo and conserved genes in gene characteristics and expression patterns.Gene ontology enrichment analysis suggested that Type I de novo genes originated from sequences related to plastid modification functions,while Type II genes were inferred to have derived from sequences related to reproductive functions.Finally,transcriptome sequencing across different tissues and developmental stages suggested that de novo genes have been evolutionarily recruited into existing regulatory networks,playing important roles in plant growth and development,which was also supported by WGCNA analysis and quantitative trait loci data.This study lays the groundwork for future research on the origins and functions of genes in Prunus and related taxa. 展开更多
关键词 prunus genomeswe conserved genes peach distinct differences observed de no gene evolution regulatory networks de novo genes transcriptome sequencing
暂未订购 下载PDF
Combination of Neuro-Fuzzy Network Models with Biological Knowledge for Reconstructing Gene Regulatory Networks 认领 引用 被引量：1
20
作者 Guixia Liu Lei Liu +3 位作者 Chunyu Liu Ming Zheng Lanying Su Chunguang Zhou 《Journal of Bionic Engineering》 SCIE EI CSCD 2011年第1期98-106,共9页
Inferring gene regulatory networks from large-scale expression data is an important topic in both cellular systems and computational biology. The inference of regulators might be the core factor for understanding actu... Inferring gene regulatory networks from large-scale expression data is an important topic in both cellular systems and computational biology. The inference of regulators might be the core factor for understanding actual regulatory conditions in gene regulatory networks, especially when strong regulators do work significantly. In this paper, we propose a novel approach based on combining neuro-fu^zy network models with biological knowledge to infer strong regulators and interrelated fuzzy rules. The hybrid neuro-fuzzy architecture can not only infer the fuzzy rules, which are suitable for describing the regulatory conditions in regulatory nctworks＋ but also explain the meaning of nodes and weight value in the neural network. It can get useful rules automatically without lhctitious judgments. At the same time, it does not add recursive layers to the model, and the model can also strengthen the relationships among genes and reduce calculation. We use the proposed approach to reconstruct a partial gene regulatory network of yeast, The results show that this approach can work effectively. 展开更多
关键词 neuro-fuzzy network biological knowledge regulators gene regulatory networks
已选0条
引用分析
参考文献
引证文献
 统计分析
检索结果
已选文献
上一页 1 2 … 11 下一页 到第 页
在线咨询 使用帮助 返回顶部 意见反馈