Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

scientific article published on 27 August 2009

Co-expression tools for plant biology: opportunities for hypothesis generation and caveats is …
instance of (P31):
review articleQ7318358
scholarly articleQ13442814

External links are
P356DOI10.1111/J.1365-3040.2009.02040.X
P698PubMed publication ID19712066
P5875ResearchGate publication ID227700549

P50authorGeorge W. BasselQ40932011
Dirk SteinhauserQ43134318
Björn UsadelQ55437593
Federico Manuel GiorgiQ59531244
Amanda Froehlich ChowQ63958857
Nicholas J ProvartQ88774804
Staffan PerssonQ40038317
P2093author name stringMimi Tanimoto
Takeshi Obayashi
Marek Mutwil
P2860cites workThe mutual information: detecting and evaluating dependencies between variables.Q34973910
P433issue12
P407language of work or nameEnglishQ1860
P921main subjectbotanyQ441
hypothesis generationQ110910415
P304page(s)1633-1651
P577publication date2009-08-27
P1433published inPlant, Cell and EnvironmentQ15766307
P1476titleCo-expression tools for plant biology: opportunities for hypothesis generation and caveats
P478volume32

Reverse relations

cites work (P2860)
Q33675555*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants
Q3860678450 years of Arabidopsis research: highlights and future directions
Q38837556A Global Coexpression Network Approach for Connecting Genes to Specialized Metabolic Pathways in Plants.
Q38450915A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in Arabidopsis thaliana.
Q58566520A cancer tissue-specific FAM72 expression profile defines a novel glioblastoma multiform (GBM) gene-mutation signature
Q39383513A combination of gene expression ranking and co-expression network analysis increases discovery rate in large-scale mutant screens for novel Arabidopsis thaliana abiotic stress genes.
Q37068437A contribution to the study of plant development evolution based on gene co-expression networks
Q40117419A digital compendium of genes mediating the reversible phosphorylation of proteins in fe-deficient Arabidopsis roots
Q55450298A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system.
Q38240413A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches.
Q35648525A null model for Pearson coexpression networks
Q38487153A regulatory network-based approach dissects late maturation processes related to the acquisition of desiccation tolerance and longevity of Medicago truncatula seeds
Q40235085ALCOdb: Gene Coexpression Database for Microalgae
Q30714199ATTED-II in 2014: evaluation of gene coexpression in agriculturally important plants
Q36488613ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression
Q46245907ATTED-II in 2018: A Plant Coexpression Database based on Investigation of Statistical Property of the Mutual Rank Index
Q34566240ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants
Q21284343Algorithm-driven artifacts in median polish summarization of microarray data
Q52356479An integrated approach to infer cross-talks between intracellular protein transport and signaling pathways.
Q33955431An integrated genomic and metabolomic framework for cell wall biology in rice
Q90405779An updated gene atlas for maize reveals organ-specific and stress-induced genes
Q90629147Analysis of gene co-expression networks of phosphate starvation and aluminium toxicity responses in Populus spp
Q33358740Analysis of the arabidopsis REM gene family predicts functions during flower development.
Q35206810Annotation of gene function in citrus using gene expression information and co-expression networks
Q47382803Application of the Gini correlation coefficient to infer regulatory relationships in transcriptome analysis.
Q38494473Arabidopsis thaliana mTERF proteins: evolution and functional classification
Q38508445Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm
Q30878072AtCAST3.0 update: a web-based tool for analysis of transcriptome data by searching similarities in gene expression profiles
Q47745452BAR expressolog identification: expression profile similarity ranking of homologous genes in plant species
Q92065187BioHackathon 2015: Semantics of data for life sciences and reproducible research
Q37112910Bioinformatics Approach in Plant Genomic Research
Q36079515Bioinformatics Tools for Exploring the SUMO Gene Network.
Q38460232Brief Exercises Affect Gene Expression in Circulating Monocytes
Q31159224CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data
Q28818101COEXPEDIA: exploring biomedical hypotheses via co-expressions associated with medical subject headings (MeSH)
Q38496806CORNET 2.0: integrating plant coexpression, protein-protein interactions, regulatory interactions, gene associations and functional annotations
Q33522353CORNET: a user-friendly tool for data mining and integration
Q30869228COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems
Q64971412COXPRESdb v7: a gene coexpression database for 11 animal species supported by 23 coexpression platforms for technical evaluation and evolutionary inference.
Q30579745COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals.
Q41580634COXPRESdb: a database to compare gene coexpression in seven model animals
Q48157947Cell cycle-regulated PLEIADE/AtMAP65-3 links membrane and microtubule dynamics during plant cytokinesis
Q34465343Characterization and co-expression analysis of WRKY orthologs involved in responses to multiple abiotic stresses in Pak-choi (Brassica campestris ssp. chinensis)
Q28596237Characterization of CIPK Family in Asian Pear (Pyrus bretschneideri Rehd) and Co-expression Analysis Related to Salt and Osmotic Stress Responses
Q90453936Characterization of PP2A-A3 mRNA expression and growth patterns in Arabidopsis thaliana under drought stress and abscisic acid
Q89453194Chlamydomonas CHT7 is Required for an Effective Quiescent State by Regulating Nutrient-responsive Cell Cycle Gene Expression
Q36933227Cloning, Functional Characterization, and Catalytic Mechanism of a Bergaptol O-Methyltransferase from Peucedanum praeruptorum Dunn
Q33768420Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene
Q59806873Co-expression Gene Network Analysis and Functional Module Identification in Bamboo Growth and Development
Q38099400Co-expression analysis as tool for the discovery of transport proteins in photorespiration
Q38496694Co-expression analysis identifies CRC and AP1 the regulator of Arabidopsis fatty acid biosynthesis
Q38060721Co-expression and co-responses: within and beyond transcription
Q38014434Co-expression of cell-wall related genes: new tools and insights
Q35896689CoExpNetViz: Comparative Co-Expression Networks Construction and Visualization Tool
Q37728930Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways
Q34450698Colinearity and similar expression pattern of rice DREB1s reveal their functional conservation in the cold-responsive pathway
Q84387320Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function
Q38001459Comparative co-expression analysis in plant biology
Q58106975Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max
Q34325821Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana.
Q35683301Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules
Q34064362Comprehensive network analysis of anther-expressed genes in rice by the combination of 33 laser microdissection and 143 spatiotemporal microarrays
Q38651544Connectivity in gene coexpression networks negatively correlates with rates of molecular evolution in flowering plants.
Q38690437Constructing Integrated Networks for Identifying New Secondary Metabolic Pathway Regulators in Grapevine: Recent Applications and Future Opportunities.
Q38646016Construction and Optimization of a Large Gene Coexpression Network in Maize Using RNA-Seq Data.
Q31011674Construction of citrus gene coexpression networks from microarray data using random matrix theory
Q44962156Coordinated activation of cellulose and repression of lignin biosynthesis pathways in rice
Q41457751Correlation networks visualization
Q36296443Correlation of aquaporins and transmembrane solute transporters revealed by genome-wide analysis in developing maize leaf
Q38186688Cracking the Kranz enigma with systems biology.
Q38103855Current challenges and future potential of tomato breeding using omics approaches
Q33587522Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis.
Q37184355Differential Network Analysis Reveals Evolutionary Complexity in Secondary Metabolism of Rauvolfia serpentina over Catharanthus roseus
Q35186754Discovering functional modules across diverse maize transcriptomes using COB, the Co-expression Browser.
Q33564134Distinct pathways mediate the sorting of tail-anchored proteins to the plastid outer envelope
Q34077081Effects of abiotic stress on plants: a systems biology perspective
Q26852357Elucidating gene function and function evolution through comparison of co-expression networks of plants
Q33787477Engineering crassulacean acid metabolism to improve water-use efficiency
Q34472586Evolution and functional implications of the tricarboxylic acid cycle as revealed by phylogenetic analysis
Q34544101Evolution of herbivore-induced early defense signaling was shaped by genome-wide duplications in Nicotiana
Q42290576Evolutionary Analysis of DELLA-Associated Transcriptional Networks.
Q44544071Evolutionary analyses of non-family genes in plants
Q38498511Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches
Q38724314Expression atlas and comparative coexpression network analyses reveal important genes involved in the formation of lignified cell wall in Brachypodium distachyon
Q46513781FamNet: A Framework to Identify Multiplied Modules Driving Pathway Expansion in Plants.
Q36364750From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data
Q34012502Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets
Q35254016GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response
Q30847231GENIUS: web server to predict local gene networks and key genes for biological functions.
Q34334099GabiPD - The GABI Primary Database integrates plant proteomic data with gene-centric information
Q55218928Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Camellia sinensis) Using 'Omics'-Based Network Approaches: A Future Perspective.
Q39986354Gene co-expression analyses: an overview from microarray collections in Arabidopsis thaliana
Q84179075Gene coexpression network alignment and conservation of gene modules between two grass species: maize and rice
Q31027057Gene coexpression network analysis as a source of functional annotation for rice genes
Q39795239Gene coexpression network analysis of oil biosynthesis in an interspecific backcross of oil palm.
Q46640740Gene mapping and functional analysis of the novel leaf color gene SiYGL1 in foxtail millet [Setaria italica (L.) P. Beauv].
Q51791978Gene-sharing networks reveal organizing principles of transcriptomes in Arabidopsis and other multicellular organisms.
Q35605049Genetic variation of transgenerational plasticity of offspring germination in response to salinity stress and the seed transcriptome of Medicago truncatula
Q36775971Genome-Wide Analysis Indicates Lineage-Specific Gene Loss during Papilionoideae Evolution
Q64080384Genome-Wide Analysis of Glycoside Hydrolase Family 1 β-glucosidase Genes in and Their Potential Role in Pollen Development
Q38947487Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants
Q34372952Genome-scale identification of cell-wall related genes in Arabidopsis based on co-expression network analysis
Q88088650Genome-wide analyses of ATP sulfurylase (ATPS) genes in higher plants and expression profiles in sorghum (Sorghum bicolor) under cadmium and salinity stresses
Q35803809Genome-wide analysis of overlapping genes regulated by iron deficiency and phosphate starvation reveals new interactions in Arabidopsis roots
Q36240692Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.).
Q34645021Genome-wide co-expression analysis predicts protein kinases as important regulators of phosphate deficiency-induced root hair remodeling in Arabidopsis.
Q38879349Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.).
Q54976461Genome-wide identification and characterization of the RIO atypical kinase family in plants.
Q35035044Genome-wide network model capturing seed germination reveals coordinated regulation of plant cellular phase transitions
Q42379276Genome-wide trait-trait dynamics correlation study dissects the gene regulation pattern in maize kernels
Q38040102Glutamine synthetase in legumes: recent advances in enzyme structure and functional genomics
Q37000098Golgi-localized STELLO proteins regulate the assembly and trafficking of cellulose synthase complexes in Arabidopsis
Q34294495Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes
Q35918335Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis
Q35805965Identification of Photosynthesis-Associated C4 Candidate Genes through Comparative Leaf Gradient Transcriptome in Multiple Lineages of C3 and C4 Species.
Q59164690Identification of a novel type of WRKY transcription factor binding site in elicitor-responsive cis-sequences from Arabidopsis thaliana
Q36584948Identification of conserved drought stress responsive gene-network across tissues and developmental stages in rice
Q34302898Identification of metagenes and their interactions through large-scale analysis of Arabidopsis gene expression data
Q24616939Identification of the 2-hydroxyglutarate and isovaleryl-CoA dehydrogenases as alternative electron donors linking lysine catabolism to the electron transport chain of Arabidopsis mitochondria
Q33364869Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions
Q36866248Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system.
Q30797459Improving clustering with metabolic pathway data
Q35008864Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways
Q40496536Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways
Q38022502Inferring gene functions through dissection of relevance networks: interleaving the intra- and inter-species views
Q64095517Infrastructures of systems biology that facilitate functional genomic study in rice
Q34637593Integrated proteomics and metabolomics of Arabidopsis acclimation to gene-dosage dependent perturbation of isopropylmalate dehydrogenases
Q35158705Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes
Q36360290Integration of a Decrescent Transcriptome and Metabolomics Dataset of Peucedanum praeruptorum to Investigate the CYP450 and MDR Genes Involved in Coumarins Biosynthesis and Transport
Q38324013Integration of bioinformatics and synthetic promoters leads to the discovery of novel elicitor-responsive cis-regulatory sequences in Arabidopsis
Q24607271KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data
Q51350573LASSO modeling of the Arabidopsis thaliana seed/seedling transcriptome: a model case for detection of novel mucilage and pectin metabolism genes.
Q31123719Large-Scale Public Transcriptomic Data Mining Reveals a Tight Connection between the Transport of Nitrogen and Other Transport Processes in Arabidopsis
Q41965297Large-scale co-expression approach to dissect secondary cell wall formation across plant species
Q27015436Learning from Co-expression Networks: Possibilities and Challenges
Q38199676Lignin, mitochondrial family, and photorespiratory transporter classification as case studies in using co-expression, co-response, and protein locations to aid in identifying transport functions
Q44609278Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis.
Q38648542Maize network analysis revealed gene modules involved in development, nutrients utilization, metabolism, and stress response.
Q35034223Mediated plastid RNA editing in plant immunity
Q50027416Melonet-DB, a Grand RNA-Seq Gene Expression Atlas in Melon (Cucumis melo L.).
Q26795729Modelling signaling networks underlying plant defence
Q38193772Modelling transcriptional networks in leaf senescence
Q36016745Modular reorganization of the global network of gene regulatory interactions during perinatal human brain development.
Q26764945More effort - more results: recent advances in integrative 'omics' data analysis
Q53696158MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants.
Q50099223NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples.
Q38075582Network analysis for gene discovery in plant-specialized metabolism
Q58249849Network approaches to the genetic dissection of phenotypes in animals and humans
Q38914293Networks of ProteinProtein Interactions: From Uncertainty to Molecular Details.
Q31113924New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana
Q35148067New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes
Q33776476New perspectives on glutamine synthetase in grasses
Q35500802No3CoGP: non-conserved and conserved coexpressed gene pairs
Q35591942Novel disease susceptibility factors for fungal necrotrophic pathogens in Arabidopsis
Q33561812ORTom: a multi-species approach based on conserved co-expression to identify putative functional relationships among genes in tomato
Q46299533Omics approaches to study gene regulatory networks for development in echinoderms
Q83265557On the discordance of metabolomics with proteomics and transcriptomics: coping with increasing complexity in logic, chemistry, and network interactions scientific correspondence
Q57294394PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in
Q37508331Pan- and core- network analysis of co-expression genes in a model plant.
Q35084716Perspectives on Systematic Analyses of Gene Function in Arabidopsis thaliana: New Tools, Topics and Trends
Q38978558Phylogenomic analysis of gene co-expression networks reveals the evolution of functional modules.
Q91012550Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings
Q55518732PhytoNet: comparative co-expression network analyses across phytoplankton and land plants.
Q91856140PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System
Q39093179PlaNet: Comparative Co-Expression Network Analyses for Plants
Q38502841PlaNet: combined sequence and expression comparisons across plant networks derived from seven species
Q38438346Plant genome and transcriptome annotations: from misconceptions to simple solutions
Q38622214Plants in silico: why, why now and what?--an integrative platform for plant systems biology research
Q33750757Predicting genome-wide redundancy using machine learning
Q33905868Prospecting for genes involved in transcriptional regulation of plant defenses, a bioinformatics approach
Q64912648Putting primary metabolism into perspective to obtain better fruits.
Q42363282RECoN: Rice Environment Coexpression Network for Systems Level Analysis of Abiotic-Stress Response.
Q42773717RNA-seq of Arabidopsis pollen uncovers novel transcription and alternative splicing
Q30000331Re-analysis of RNA-seq transcriptome data reveals new aspects of gene activity in Arabidopsis root hairs
Q64232306Recent advances in gene function prediction using context-specific coexpression networks in plants
Q30584792Reverse engineering: a key component of systems biology to unravel global abiotic stress cross-talk
Q47650681RiceAntherNet: a gene co-expression network for identifying anther and pollen development genes.
Q34456107RiceXPro: a platform for monitoring gene expression in japonica rice grown under natural field conditions
Q39190028Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.).
Q33931718Salt stress and senescence: identification of cross-talk regulatory components.
Q92566680Sulphur systems biology-making sense of omics data
Q30000845Systematic identification of functional plant modules through the integration of complementary data sources
Q38056560Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks
Q37860973Systems biology approaches to abscisic acid signaling
Q97066818TeaCoN: a database of gene co-expression network for tea plant (Camellia sinensis)
Q39093205The Bio-Analytic Resource for Plant Biology
Q38198021The ER quality control and ER associated degradation machineries are vital for viral pathogenesis
Q44876881The MORPH algorithm: ranking candidate genes for membership in Arabidopsis and tomato pathways.
Q89039561The Pentatricopeptide Repeat Gene Family in Salvia miltiorrhiza: Genome-Wide Characterization and Expression Analysis
Q41809274The effects of graded levels of calorie restriction: VII. Topological rearrangement of hypothalamic aging networks
Q38076753The evolution of phenylpropanoid metabolism in the green lineage
Q46855409The functional network of the Arabidopsis plastoglobule proteome based on quantitative proteomics and genome-wide coexpression analysis
Q41468277The phenylpropanoid pathway is controlled at different branches by a set of R2R3-MYB C2 repressors in grapevine.
Q41343379The plant transcriptome-from integrating observations to models
Q34310009The roots of plant defenses: integrative multivariate analyses uncover dynamic behaviors of gene and metabolic networks of roots elicited by leaf herbivory
Q57467438Unravelling the complex trait of seed quality: using natural variation through a combination of physiology, genetics and -omics technologies
Q42277382Use of the growing environment as a source of variation to identify the quantitative trait transcripts and modules of co-expressed genes that determine chlorogenic acid accumulation
Q30486550VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine).
Q45905497VirtualPlant: a software platform to support systems biology research.
Q41002014Volatile Glycosylation in Tea Plants: Sequential Glycosylations for the Biosynthesis of Aroma β-Primeverosides Are Catalyzed by Two Camellia sinensis Glycosyltransferases.

Search more.