Discovery of core biotic stress responsive genes in Arabidopsis by weighted gene co-expression network analysis

scientific article published on 2 March 2015

Discovery of core biotic stress responsive genes in Arabidopsis by weighted gene co-expression network analysis is …
instance of (P31):
scholarly articleQ13442814

External links are
P819ADS bibcode2015PLoSO..1018731A
P356DOI10.1371/JOURNAL.PONE.0118731
P932PMC publication ID4346582
P698PubMed publication ID25730421
P5875ResearchGate publication ID273763663

P50authorDario CantuQ56999532
P2093author name stringBarbara Blanco-Ulate
Katherine C H Amrine
P2860cites workWGCNA: an R package for weighted correlation network analysisQ21284194
Genomic gene clustering analysis of pathways in eukaryotesQ24561729
AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factorsQ24790976
Calcium-dependent protein kinases: hubs in plant stress signaling and developmentQ26825246
Transcriptional regulatory networks in Saccharomyces cerevisiaeQ27860846
Network biology: understanding the cell's functional organizationQ27861027
Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expressionQ28343758
AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studiesQ28743772
Lethality and centrality in protein networksQ29547267
Error and attack tolerance of complex networksQ29547268
Cytoscape 2.8: new features for data integration and network visualizationQ29547471
A general framework for weighted gene co-expression network analysisQ29617580
Host-microbe interactions: shaping the evolution of the plant immune responseQ29617734
Plant immunity: towards an integrated view of plant-pathogen interactionsQ30004699
Early nuclear events in plant defence signalling: rapid gene activation by WRKY transcription factorsQ30763480
Overexpression of AtWRKY28 and AtWRKY75 in Arabidopsis enhances resistance to oxalic acid and Sclerotinia sclerotiorumQ50923989
Computing topological parameters of biological networksQ51900389
MAP kinase signalling cascade in Arabidopsis innate immunityQ52594626
The transcriptome of Arabidopsis thaliana during systemic acquired resistanceQ54027920
Reactive oxygen species signaling in response to pathogensQ57748274
Conservation and coevolution in the scale-free human gene coexpression networkQ80392034
Transcriptome analysis of the barley-Fusarium graminearum interactionQ83147688
Photosynthesis, photorespiration, and light signalling in defence responsesQ37979171
Hormonal modulation of plant immunityQ38007563
Impacts of Resistance Gene Genetics, Function, and Evolution on a Durable FutureQ38107531
Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses.Q38290951
A GCC element and a G-box motif participate in ethylene-induced expression of the PRB-1b geneQ38296991
Developmental and stimulus-induced expression patterns of Arabidopsis calmodulin-like genes CML37, CML38 and CML39.Q38300682
Transgenic expression of MYB15 confers enhanced sensitivity to abscisic acid and improved drought tolerance in Arabidopsis thalianaQ38973695
The response regulator 2 mediates ethylene signalling and hormone signal integration in Arabidopsis.Q39949321
Plant 'pathogenesis-related' proteins and their role in defense against pathogens.Q40803299
Fast R Functions for Robust Correlations and Hierarchical ClusteringQ42239626
OXI1 kinase is necessary for oxidative burst-mediated signalling in ArabidopsisQ42457720
The transcriptional innate immune response to flg22. Interplay and overlap with Avr gene-dependent defense responses and bacterial pathogenesisQ42462694
Biotic stress globally downregulates photosynthesis genesQ42659578
Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringaeQ44302174
The Arabidopsis glucosyltransferase UGT76B1 conjugates isoleucic acid and modulates plant defense and senescenceQ44426370
Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infectionQ44576820
Calcium/calmodulin up-regulates a cytoplasmic receptor-like kinase in plantsQ45005926
A mutation in an Arabidopsis ribose 5-phosphate isomerase reduces cellulose synthesis and is rescued by exogenous uridine.Q47180779
Evidence for a positive regulatory role of strawberry (Fragaria x ananassa) Fa WRKY1 and Arabidopsis At WRKY75 proteins in resistance.Q47723229
Identification of genes encoding receptor-like protein kinases as possible targets of pathogen- and salicylic acid-induced WRKY DNA-binding proteins in ArabidopsisQ47803594
Improved scoring of functional groups from gene expression data by decorrelating GO graph structureQ31036410
Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networksQ33235411
Eigengene networks for studying the relationships between co-expression modulesQ33306760
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thalianaQ33801141
The LSD1-interacting protein GILP is a LITAF domain protein that negatively regulates hypersensitive cell death in ArabidopsisQ33883661
Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expressionQ33893213
Molecular responses to dehydration and low temperature: differences and cross-talk between two stress signaling pathwaysQ33932925
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors.Q34381452
GeneFriends: an online co-expression analysis tool to identify novel gene targets for aging and complex diseases.Q34435173
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update.Q34456259
Significance of inducible defense-related proteins in infected plants.Q34511918
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R.Q34714933
Transcription factors in plant defense and stress responsesQ34787026
An extracellular subtilase switch for immune priming in Arabidopsis.Q34789304
Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networksQ34825012
Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathwaysQ35008864
Systematic identification of cell-wall related genes in Populus based on analysis of functional modules in co-expression networkQ35149339
Expression-based network biology identifies immune-related functional modules involved in plant defenseQ35180026
Conservation and evolution of gene coexpression networks in human and chimpanzee brainsQ35215128
An Arabidopsis gene network based on the graphical Gaussian model.Q36098278
Constructing transcriptional regulatory networksQ36184323
COXPRESdb: a database of coexpressed gene networks in mammalsQ36454116
Seduced by the dark side: integrating molecular and ecological perspectives on the influence of light on plant defence against pests and pathogens.Q36473259
Transcript profiling in host-pathogen interactionsQ36811551
Networks of WRKY transcription factors in defense signaling.Q36888216
Making sense of hormone crosstalk during plant immune responsesQ37186947
Importing ArrayExpress datasets into R/BioconductorQ37295100
Role of plant hormones in plant defence responsesQ37350835
Primary metabolism and plant defense--fuel for the fireQ37434543
Networking by small-molecule hormones in plant immunity.Q37450759
The role of WRKY transcription factors in plant immunityQ37472672
Photosynthetic and respiratory changes in leaves of poplar elicited by rust infectionQ37655298
The language of calcium signalingQ37700628
Plant responses to insect herbivory: interactions between photosynthesis, reactive oxygen species and hormonal signalling pathwaysQ37900657
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P4510describes a project that usesCytoscapeQ3699942
WGCNAQ102537983
limmaQ112236343
P433issue3
P407language of work or nameEnglishQ1860
P304page(s)e0118731
P577publication date2015-03-02
P1433published inPLOS OneQ564954
P1476titleDiscovery of core biotic stress responsive genes in Arabidopsis by weighted gene co-expression network analysis
P478volume10

Reverse relations

cites work (P2860)
Q90013549Analysis of chickpea gene co-expression networks and pathways during heavy metal stress
Q47208719Cattle infection response network and its functional modules.
Q47114714Co-expression network analysis of the transcriptomes of rice roots exposed to various cadmium stresses reveals universal cadmium-responsive genes.
Q89511545Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways
Q58760196Comparative transcriptome meta-analysis of Arabidopsis thaliana under drought and cold stress
Q36115331Comparative transcriptomics of Central Asian Vitis vinifera accessions reveals distinct defense strategies against powdery mildew
Q37323863Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection.
Q64069518Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple ( × )
Q33556217Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses
Q91063363Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis
Q42700303Identification of DNA methylation associated gene signatures in endometrial cancer via integrated analysis of DNA methylation and gene expression systematically.
Q91062458Identification of key genes involved in the biosynthesis of triterpenic acids in the mint family
Q33364869Identifying gene coexpression networks underlying the dynamic regulation of wood-forming tissues in Populus under diverse environmental conditions
Q40496536Inference of Longevity-Related Genes from a Robust Coexpression Network of Seed Maturation Identifies Regulators Linking Seed Storability to Biotic Defense-Related Pathways
Q48062767Integrated omics analysis of specialized metabolism in medicinal plants
Q55237555Integrating Phylogenetic and Network Approaches to Study Gene Family Evolution: The Case of the AGAMOUS Family of Floral Genes.
Q38453662Joint genetic and network analyses identify loci associated with root growth under NaCl stress in Arabidopsis thaliana
Q26795729Modelling signaling networks underlying plant defence
Q33844280Neofusicoccum parvum Colonization of the Grapevine Woody Stem Triggers Asynchronous Host Responses at the Site of Infection and in the Leaves
Q31113924New BAR tools for mining expression data and exploring Cis-elements in Arabidopsis thaliana
Q37018944Obligate Biotroph Pathogens of the Genus Albugo Are Better Adapted to Active Host Defense Compared to Niche Competitors
Q92640857The Nutrient Response Transcriptional Regulome of Arabidopsis
Q92448032The Use of PTI-Marker Genes to Identify Novel Compounds that Establish Induced Resistance in Rice
Q33742645The common transcriptional subnetworks of the grape berry skin in the late stages of ripening
Q40281591Transcriptomic and histological responses of African rice (Oryza glaberrima) to Meloidogyne graminicola provide new insights into root-knot nematode resistance in monocots
Q90164188WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice
Q64107095WRINKLED1 transcription factor orchestrates the regulation of carbon partitioning for C18:1 (oleic acid) accumulation in Siberian apricot kernel

Search more.