Gene coexpression arabidopsis. Arabidopsis Coexpression Tool (ACT), a gene coexpression analysis web tool for Arabidopsis thaliana, identifies genes which are correlated to a driver gene. Weighted Gene Correlation Network Analysis (WGCNA) is an R package that provides a multitude of functions for constructing and analyzing a weighted or unweighted gene coexpression network. This bug has been fixed. In this protocol, we describe the steps necessary to create a gene coexpression tree for Arabidopsis thaliana, using publicly available Affymetrix CEL microarray data. The analysis identified 149 gene co-expression modules, which we considered to be Coexpression Arabidopsis thaliana Tool (ACT), a gene coexpression analysis web tool for , iden-tifies genes which are correlated to a driver gene. English. A more holistic view of this molecular interplay will help in the further study of the regulatory mechanisms controlling Coexpressed genes tend to participate in related biological processes. Biology 11, 1019. 0] The new version provides updated coexpression data, including wheat and barley, along with a PC Details page for a more detailed understanding of individual coexpressed gene pairs. Jan 30, 2019 · A gene co-expression network of Arabidopsis was successfully constructed A total of 11,896 Arabidopsis samples were used to construct a scale-free gene co-expression network, which is a property of natural biological networks, by choosing a power of 10 (Fig. A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression. We show that all four selected Apr 12, 2021 · Many genome-wide datasets from various sources are combined to generate an integrative gene regulatory network in Arabidopsis. Currently, it is still unclear how much of this local co-expression is caused by direct transcriptional interactions, and how much is due to shared chromatin environments. Each node represents a gene, and each edge between two nodes represents a connection or association between the nodes (genes). In this protocol, we describe the Sep 2, 2024 · The molecular mechanisms underlying photoperiodic regulation of flowering time have been best characterized in Arabidopsis. Gene coexpression tools allow for the prediction of functional gene partners or the Aug 8, 2021 · Gene coexpression analysis refers to the discovery of sets of genes which exhibit similar expression patterns across multiple transcriptomic data sets, such as microarray experiment data of public repositories. Gene coexpression analysis pointed to two P450s that were coexpressed with two monoterpene synthases in flowers and were thus … Jul 10, 2021 · Gene coexpression analysis refers to the discovery of sets of genes which exhibit similar expression patterns across multiple transcriptomic data sets, such as microarray experiment data of public repositories. , Iconomidou, V. Arabidopsis thaliana is a widely studied model plant whose transcriptome has been substan … Human Gene Coexpression Analysis ToolsArabidopsis Coexpression Tools 2024. Based on the RNA sequencing dataset, we applied weighted gene co-expression network analysis (WGCNA) to identify sepal, petal, stamen, stigma and other specific modules as well as hub genes involved in specific floral organ development. Zogopoulos, V. Gene coexpression networks depict the degree of similarity Here we present a new approach, trans-organ analysis of gene co-expression networks, which offers a unique way of identifying candidates for such genes. , Papadopoulos, K. This network is used to predict and validate new transcriptional A plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa. Arabidopsis Coexpression Tool (ACT) is used for the identification of transcriptionally correlated (coexpressed) genes in Arabidopsis thaliana. Gene co-expression network analysis identifies BEH3 as a stabilizer of secondary vascular development in Arabidopsis Apr 8, 2016 · The orthologous clusters of co-expressed genes identified in poplar did not all correlate in gene expression pattern with the clusters in Arabidopsis (gene expression pattern correlated for 9 of 22 clusters). 6). Using time-series microarray data of Arabidopsis thaliana infected with Pseudomonas Abstract Fungi of the Trichoderma genus are called "biostimulants" because they promote plant growth and development and induce disease resistance. , Malatras, A. Among 181 Arabidopsis and 168 rice differentially expressed TF genes, 37 (26 novel) were up- and 16 (8 novel) were downregulated. , and Michalopoulos, I. Abstract We present a new WWW-based tool for plant gene analysis, the Arabidopsis Co-Expression Tool (ACT), based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. Those oscillations can persist under constant conditions due to regulat Sep 6, 2025 · Article Title: Trans-organ analysis of gene co-expression networks reveals a mobile long-distance regulator that balances shoot and root development in Arabidopsis Article References: Jun 1, 2021 · Gene co-expression network analysis identifies BEH3 as a stabilizer of secondary vascular development in Arabidopsis Here we present a new approach, trans-organ analysis of gene co-expression networks, which o˜ers a unique way of identifying candidates for such genes. Oct 14, 2021 · Our study provides a global view on RNA–chromatin interactions in Arabidopsis and a rich resource for future investigations of regulatory roles of RNAs in gene expression and genome organization. Because the Aug 26, 2024 · Light/dark (LD) cycles are responsible for oscillations in gene expression, which modulate several aspects of plant physiology. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. Gene network modeling and visualization are powerful tools from which biologists can derive testable hypotheses. These modules Jul 16, 2025 · Trans-organ analysis of gene co-expression networks in different tissues provides a unique method for uncovering long-distance regulation. At the module level, the Mar 18, 2022 · Coexpressed genes tend to participate in related biological processes. As described in the methods, the hierarchically clustered genes were detected iteratively by dynamic tree cut method to find Oct 21, 2009 · In this report, we attempted to find the relationship between the network topology and formation of modular structure by comparing gene co-expression networks with random networks. The network was grouped into 622 gene co-expression modules. The co-expression analysis tool allows users to identify genes whose expression patterns are correlated across selected experiments or the complete data set. Gene co-expression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGG … We present here an Arabidopsis gene co-expression network constructed using RNA-Seq datasets, which will serve as a useful resource for the Arabidopsis research community to gain insights into Arabidopsis gene interactions and functions. This approach revealed that TGA7 functions as a shoot-to-root mobile bZIP transcription factor in Arabidopsis to activate photosynthetic genes directly in shoots and nitrate-uptake-related Dec 23, 2014 · The phytohormone auxin regulates nearly all aspects of plant growth and development. We show that all four selected In Arabidopsis, a large number of genes involved in the accumulation of seed storage reserves during seed development have been characterized, but the relationship of gene expression and regulation underlying this physiological process remains Mar 1, 2017 · In the case of Arabidopsis thaliana, the reference species in plant biology, the resources available mainly consist of microarray results. May 23, 2024 · This study reports a single-cell gene co-expression network analysis performed with single-cell transcriptome datasets from Arabidopsis roots, leading to the identification of 149 gene expression programs (GEPs) that regulate the development of major root cell types and participate in cell-type-specific metabolism. The phytohormone auxin regulates nearly all aspects of plant growth and development. Using these GEPs, the authors identified the columella-specific gene NRL27 and Apr 26, 2022 · We present here an Arabidopsis gene co-expression network constructed using RNA-Seq datasets, which will serve as a useful resource for the Arabidopsis research community to gain insights into Arabidopsis gene interactions and functions. At large Background/Objectives: Genes with similar expression patterns across multiple samples are considered coexpressed, and they may participate in similar biological processes or pathways. Jun 13, 2014 · During very early stages of flower development in Arabidopsis thaliana, a series of key decisions are taken. thaliana 21,000 The Arabidopsis Gene Expression Database (AGED) is a specialized bioinformatics resource designed to provide an extensive repository of gene expression data for Arabidopsis thaliana, one of the most widely studied model organisms in plant biology. thaliana. Approaches in Gene Coexpression Analysis in Eukaryotes. The organization of gene functional modules was also investigated. 9. 09. Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about Mar 11, 2018 · A systems biology approach for transcriptome data analyses. Nov 12, 2020 · In this chapter, we will investigate some of the tools used for examining gene expression and coexpression patterns, performing promoter analyses and functional classification enrichment for sets of genes, and exploring protein–protein and protein–DNA interactions in Arabidopsis. We conducted a single-cell gene co-expression network analysis with publicly available scRNA-seq datasets of Arabidopsis roots using a SingleCellGGM algorithm. The Arabidopsis Genome Database (AGD) is an electronic database freely accessible to the public, providing comprehensive biological information about Arabidopsis thaliana, a widely studied model plant species. The orthologous clusters of co-expressed genes identified in poplar did not all correlate in gene expression pattern with the clusters in Arabidopsis (gene expression pattern correlated for 9 of 22 clusters). Jan 30, 2024 · We used conventional transcriptome and gene co-expression analyses to understand the molecular response of the plant Arabidopsis thaliana to inoculation with Trichoderma atroviride or Trichoderma Dec 23, 2014 · We analyzed gene co-expression profiles of ARF and Aux/IAA genes in different Arabidopsis tissues/organs using 65 different RNAseq datasets from the SRA (Leinonen et al, 2011). Results We analysed neighbouring genes in Arabidopsis thaliana. iScience 24, 102848. H. Using microarray data from the ArrayExpress database, we constructed an Arabidopsis gene co-expression network, termed AtGGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. A web tool to explore module information was also provided. Feb 23, 2025 · Results: The gene dendrogram was used as the basis for the creation of a new Arabidopsis coexpression tool (ACT) version (ACT2. Jun 1, 2021 · Gene co-expression network analysis identifies BEH₃ as a stabilizer of secondary vascular development in Arabidopsis Oct 21, 2009 · In this report, we attempted to find the relationship between the network topology and formation of modular structure by comparing gene co-expression networks with random networks. <i>Arabidopsis</i> Coexpression Tool (ACT), a gene coexpression analysis web tool for … Mar 8, 2006 · Summary We present a new WWW-based tool for plant gene analysis, the Arabidopsis Co-Expression Tool (act), based on a large Arabidopsis thaliana microarray data set obtained from the Nottingham Arabidopsis Stock Centre. The Dec 8, 2020 · Article Open access Published: 08 December 2020 Co-expression network analysis of protein phosphatase 2A (PP2A) genes with stress-responsive genes in Arabidopsis thaliana reveals 13 key regulators The cytochrome P450 family encompasses the largest family of enzymes in plant metabolism, and the functions of many of its members in Arabidopsis thaliana are still unknown. We Oct 21, 2009 · The cell cycle module orchestrated the coordinated expression of hundreds of genes involved in cell cycle, DNA metabolism, and cytoskeleton organization and biogenesis. Apr 15, 2011 · In this study, the Arabidopsis gene coexpression network was constructed using the ATTED-II data, and thereafter a subgraph-induced approach and clique-finding algorithm were used to extract gene coexpression groups from the gene coexpression network. Gene coexpression tools allow for the prediction of functional gene partners or the May 1, 2024 · Gene co-expression network analysis in areca floral organ and the potential role of the AcMADS17 and AcMADS23 in transgenic Arabidopsis Feb 23, 2025 · Gene coexpression tools allow for the prediction of functional gene partners or the assignment of roles to genes of unknown function. In this approach, a set of genes with known functions, termed as guide genes (or bait genes), were used to query the gene co-expression network. Amrine, Barbara Blanco-Ulate, Dario Cantu * One such coexpression database for Arabidopsis, ATTED-II, has the unique aspect of network representation of gene coexpression in addition to a simple gene list representation (12). Oct 25, 2008 · ATTED-II () is a database of gene coexpression in Arabidopsis that can be used to design a wide variety of experiments, including the prioritization of genes for functional identification or for studies of regulatory relationships. Gene coexpression networks depict the degree of similarity between the expression profiles of all genes in a set of samples. We also compared the AGCN constructed in this study with a graphical Gaussian model (GGM) based Arabidopsis gene network. In this species, the gene CONSTANS (CO) is a key integrator of circadian clock activity and photoreceptor signals to control photoperiodic flowering (Takagi et al. 27 [ver 12. With the help of this network, we identified global and stress-specific modules of coexpressed genes and were able to uncover transcriptional regulators potentially associated with nutrient responses. (2022). To provide information at a high enough spatial resolution to indicate possible heteromerization, a modified single-cell sampling technique was developed, allowing uncontaminated samples to be obtained. Hence, the present study was aimed at employing Weighted Gene Correlation Network Analysis (WGCNA) to construct a gene coexpression network (GCN) for Arabidopsis SE and then identifying highly correlated gene modules to uncover the hub genes associated with SE that may serve as potential molecular targets. Based on the current model in Arabidopsis thaliana, Auxin/indole-3-acetic acid (Aux/IAA) proteins repress auxin-inducible genes by inhibiting auxin response Mar 3, 2022 · Coexpressed genes tend to participate in related biological processes. Gene coexpression analysis allows the discovery of functional gene partners or the assignment of biological roles to genes of unknown function. In this protocol, we describe the steps We have developed a modification of the single-cell sampling technique to investigate GLR co-expression, and thus potential heteromer formation, in single cells of Arabidopsis thaliana leaves. By recombinant expression in yeast (Saccharomyces cerevisiae) and in planta we demonstrate that all four genes contribute to a thus far overlooked and complex linalool metabolism occurring in the flowers of Arabidopsis. Experimental evidence sugges … Feb 9, 2015 · Gene co-expression networks provide an important tool for systems biology studies. , Tsotra, I. Oct 10, 2016 · Abstract Plant defense responses to pathogens involve massive transcriptional reprogramming. , 2023 ). We used conventional transcriptome and gene co-expression analyses to understand the molecular response of the plant Arabidopsis thaliana to inoculation with Trichoderma atroviride or Trichoderma virens. The Arabidopsis gene co-expression network constructed based on entire collection of Arabidopsis RNA-Seq datasets at NCBI thus represents a multitude of genotypes and conditions for A. Based on the current model in Arabidopsis thaliana, Auxin/indole-3-acetic acid (Aux/IAA) proteins repress auxin-inducible genes by inhibiting auxin response transcription factors (ARFs). , Saxami, G. Mar 5, 2008 · In this study, we characterized the expression patterns of the AtGLR gene family in three different cell types of mature Arabidopsis leaves. Apr 26, 2022 · Here, we leveraged the publicly available, information-rich RNA-Seq datasets of the model plant Arabidopsis thaliana to construct a gene co-expression network, which was partitioned into clusters or modules that harbor genes correlated by expression. L. Recently, differential coexpression analysis has been developed to study the rewiring of gene networks through microarray data, which is becoming an important complement to traditional differential expression analysis. Primary microarray data from ATH1 Affymetrix platform were processed with Single-Channel Array Normaliza-tion algorithm and combined to produce a coexpression tree which contains A. The transcriptional landscape of the plant Jan 16, 2022 · Gene co-expression analysis is a data analysis technique that helps identify groups of genes with similar expression patterns across several different conditions. Aug 20, 2021 · Arabidopsis Coexpression Tool (ACT), a gene coexpression analysis web tool for Arabidopsis thaliana, identifies genes which are correlated to a driver gene. We collected microarray data from National Center for Biotechnology Information Gene Expression Omnibus Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis Jun 8, 2023 · Here, transcriptomes of Arabidopsis and rice were analyzed to computationally determine TFs and microRNAs that are differentially responsive to cold treatment, and their co-expression networks were established. 1 a, b). The cytochrome P450 family encompasses the largest family of enzymes in plant metabolism, and the functions of many of its members in Arabidopsis thaliana are still unknown. 1). Gene coexpression analysis in Arabidopsis thaliana based on public microarray data. The Arabidopsis RVE4 and RVE8 transcription factors function in the regulation of circadian clock–related target genes under normal temperature conditions but Genes whose expression levels rise and fall similarly in a large set of samples, may be considered coexpressed. SUMMARY Coexpressed genes tend to participate in related biological processes. Mar 2, 2015 · Intricate signal networks and transcriptional regulators translate the recognition of pathogens into defense responses. 15 [Bug fix] The coexpression z-score of a guide gene was incorrectly duplicated in the reference column (s) of a paralog gene (s) in the same species. This database serves a multitude of purposes, including fundamental research, disease analysis and treatment, drug discovery, plant nutrition, and population genetics. Mar 2, 2015 · Abstract Intricate signal networks and transcriptional regulators translate the recognition of pathogens into defense responses. In this protocol, we describe the steps necessary to create a gene coexpression tree for Arabi-dopsis thaliana, using publicly available Affymetrix CEL microarray data May 1, 2024 · Gene co-expression network analysis in areca floral organ and the potential role of the AcMADS17 and AcMADS23 in transgenic Arabidopsis Feb 14, 2019 · These results define gene expression patterns and coexpression networks associated with embryogenesis in Arabidopsis and provide a framework for hypothesis generation and functional validation of the molecular mechanisms governing embryogenesis. Sets of differentially expressed genes (DEGs) of interest along with publicly available information (left) can be combined to construct co-expression gene networks (center). A. The dendrogram contains 21,273 leaves, each one corresponding to First, we benchmarked the prediction performance on recently characterized Arabidopsis thaliana genes, and showed that our method outperforms state-of-the-art expression-based approaches. Oct 21, 2009 · Results We constructed a genome-wide Arabidopsis gene co-expression network (AGCN) by using 1094 microarrays. A more holistic view of this molecular interplay will help in the further study of the regulatory mechanisms controlling Sep 27, 2019 · Based on these genes, we generated a nutrient response gene coexpression network for the model plant Arabidopsis. Some studies involved construction of coexpression networks, a popular In detecting gene functional modules (or clusters) from gene co-expression networks, a guide-gene approach is commonly used. Aug 12, 2024 · Single-cell RNA-sequencing datasets of Arabidopsis roots have been generated, but related comprehensive gene co-expression network analyses are lacking. Feb 23, 2025 · Background/Objectives: Genes with similar expression patterns across multiple samples are considered coexpressed, and they may participate in similar biological processes or pathways. We constructed a genome-wide Arabidopsis gene co-expression network (AGCN) by using 1094 microarrays. Arabidopsis Coexpression Tool (ACT), a gene Jul 16, 2025 · Request PDF | Trans-organ analysis of gene co-expression networks reveals a mobile long-distance regulator that balances shoot and root development in Arabidopsis | Long-distance regulation Mar 2, 2015 · RESEARCH ARTICLE Discovery of Core Biotic Stress Responsive Genes in Arabidopsis by Weighted Gene Co-Expression Network Analysis Katherine C. Aug 31, 2021 · Here, we identified a new cambium-related regulatory module through co-expression network analysis using multiple transcriptome datasets obtained from an ectopic vascular cell transdifferentiation system using Arabidopsis cotyledons, Vascular cell Induction culture System Using Arabidopsis Leaves (VISUAL). A comprehensive network of the Arabidopsis transcriptome was analyzed and may serve as a valuable resource for candidate gene function investigations. Mar 16, 2010 · Background In all eukaryotic species examined, genes that are chromosomal neighbours are more similar in their expression than random gene pairs. These transcription factors bind specifically to auxin-responsive cis-acting elements that are frequently found in the promot-ers of early auxin-responsive genes. Gene coexpression analysis pointed to two P450s that were coexpressed with two monoterpene synthases in flowers and were thus predicted to be involved in monoterpenoid metabolism. 2022. This work was conducted to Feb 18, 2016 · Gene co-expression analyses: an overview from microarray collections in Arabidopsis thaliana Pasquale Di Salle, Guido Incerti, Chiara Colantuono, Dec 16, 2016 · Genome-wide gene expression experiments have been performed using the model plant Arabidopsis during the last decade. By means of these techniques, different groups have been able to assign putative metabolic pathways and. ACT: A tool for gene coexpression analysis in Arabidopsis thaliana. Gene coexpression In Arabidopsis, ARFs are encoded by a large gene family containing 22 members. In this study, we carried out a gene co-expression analysis of all currently publicly available microarray data, which were generated in experiments that studied the interaction of the model plant Arabidopsis thaliana with microbial pathogens. Results are We have investigated reasons for coexpression of neighboring genes in Arabidopsis, and our evidence suggests that orientation of gene pairs plays a significant role, with potential sharing of regulatory elements in divergently transcribed genes. How do I cite Arabidopsis Coexpression Tool? About TAIR The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. The AGD is We confirm their tight coexpression and show that it is at its highest during anthesis in the stamen filaments. Jun 2, 2011 · Background In Arabidopsis, a large number of genes involved in the accumulation of seed storage reserves during seed development have been characterized, but the relationship of gene expression and regulation underlying this physiological process remains poorly understood. In the AGCN, 382 hub genes formed a clique, and they were densely connected only to a small subset of the network. Further Reading: The Arabidopsis network is comprised of 21,332 nodes and 36,877,224 edges. We then analyzed the topological properties of AGCN and partitioned the network into modules by using an efficient graph clustering algorithm. This work was conducted Plants have evolved to develop resilient systems to survive in extreme temperature conditions by inducing the expression of numerous genes. Indeed, the position and the basic patterning of new flowers are determined in less than 4 Nov 27, 2013 · Abstract The cytochrome P450 family encompasses the largest family of enzymes in plant metabolism, and the functions of many of its members in Arabidopsis thaliana are still unknown. Gene coexpression analysis refers to the en masse discovery of coexpressed genes from a large variety of transcriptomic experiments. These data can be reused for research on gene function through a systematic analy-sis of gene co-expression relationships. Oct 10, 2016 · Using time-series microarray data of Arabidopsis thaliana infected with Pseudomonas syringae, we analyzed Arabidopsis defense responses to P. Here, we report updates Coexpression networks are generally defined as undirected and weighted gene connections based on gene expression patterns where nodes and edges represent genes and coexpression connections, respectively. syringae through differential coexpression analysis. Jun 8, 2023 · Here, transcriptomes of Arabidopsis and rice were analyzed to computationally determine TFs and microRNAs that are differentially responsive to cold treatment, and their co-expression networks were established. STAR Protoc 3, 101208. After a general overview of such resources, we tested and compared the results they offer for gene co-expression analysis. Background/Objectives: Genes with similar expression patterns across multiple samples are considered coexpressed, and they may participate in similar biological processes or pathways. Arabidopsis thaliana is a widely studied model plant whose transcriptome has been substantially profiled in various tissues, development stages and other conditions. The syntenic and expression patterns of AcMADS-box genes were analyzed in detail. uxvhut gcglt 3tz 1twxx r7o2h szkr m8x fpmj ej eitn