R39D13 last accessed: 2022-11-04

plexdb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798

Other names: Plant Expression Database, plexdb

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic, physical, and pathway data.

Webpage:

http://www.plexdb.org/

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Name: Other

Publications:

Publications
More detailed information about this field from each metasource.

PLEXdb: gene expression resources for plants and plant pathogens
PMID: 22084198
metasource: Fairsharing.org
version: FAIRsharing.org: PLEXdb; PLEXdb; DOI: https://doi.org/10.25504/FAIRsharing.8pjgwx; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798

BarleyBase/PLEXdb
PMID: 18287702
metasource: Fairsharing.org
version: FAIRsharing.org: PLEXdb; PLEXdb; DOI: https://doi.org/10.25504/FAIRsharing.8pjgwx; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

http://dx.doi.org/10.1093/nar/GKR938
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

PLEXdb: gene expression resources for plants and plant pathogens PubMed citations: 123.

123 articles citing: PLEXdb: gene expression resources for plants and plant pathogens

Interplay between gene expression and gene architecture as a consequence of gene and genome duplications: evidence from metabolic genes of Arabidopsis thaliana. PMID:35722515
Characterization of the heterotrimeric G protein gene families in Triticum aestivum and related species. PMID:35463045
Genetic Bases of Complex Traits: From Quantitative Trait Loci to Prediction. PMID:35451771
Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. PMID:34721467
Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence. PMID:34638885
Comparison of Transcriptional Response of C3 and C4 Plants to Drought Stress Using Meta-Analysis and Systems Biology Approach. PMID:34276729
Reinvestigation of THOUSAND-GRAIN WEIGHT 6 grain weight genes in wheat and rice indicates a role in pollen development rather than regulation of auxin content in grains. PMID:33687498
MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. PMID:33240618
Molecular Evolution of Maize Ascorbate Peroxidase Genes and Their Functional Divergence. PMID:33076444
Isolation of novel citrus and plum fruit promoters and their functional characterization for fruit biotechnology. PMID:32819338
Taxonomically Restricted Wheat Genes Interact With Small Secreted Fungal Proteins and Enhance Resistance to Septoria Tritici Blotch Disease. PMID:32477375
Insight Into the Prospects for the Improvement of Seed Starch in Legume-A Review. PMID:31736985
Transcription factors involved in abiotic stress responses in Maize (Zea mays L.) and their roles in enhanced productivity in the post genomics era. PMID:31328030
Overexpression of a soybean YABBY gene, GmFILa, causes leaf curling in Arabidopsis thaliana. PMID:31159746
Genome-Wide Identification and Characterization of the ALOG Domain Genes in Rice. PMID:30923712
Infrastructures of systems biology that facilitate functional genomic study in rice. PMID:30874968
Diffusible signal factor (DSF)-mediated quorum sensing modulates expression of diverse traits in Xanthomonas citri and responses of citrus plants to promote disease. PMID:30654743
Genome-wide identification and characterization of gene family for RWP-RK transcription factors in wheat (Triticum aestivum L.). PMID:30540790
Molecular evolution and expression divergence of three key Met biosynthetic genes in plants: CGS, HMT and MMT. PMID:30533310
The Maize NBS-LRR Gene ZmNBS25 Enhances Disease Resistance in Rice and Arabidopsis. PMID:30065743
Pathway Editing Targets for Thiamine Biofortification in Rice Grains. PMID:30042775
Genome-wide identification and characterization of the RIO atypical kinase family in plants. PMID:29892951
Molecular Evolution and Expression Divergence of HMT Gene Family in Plants. PMID:29677135
Inter-genome comparison of the Quorn fungus Fusarium venenatum and the closely related plant infecting pathogen Fusarium graminearum. PMID:29673315
Comparative Genomics of Non-TNL Disease Resistance Genes from Six Plant Species. PMID:28973974
RiceMetaSys for salt and drought stress responsive genes in rice: a web interface for crop improvement. PMID:28964253
Functional divergence and origin of the DAG-like gene family in plants. PMID:28720816
Molecular Characterization, Gene Evolution, and Expression Analysis of the Fructose-1, 6-bisphosphate Aldolase (FBA) Gene Family in Wheat (Triticum aestivum L.). PMID:28659962
The Evolutionary Basis of Translational Accuracy in Plants. PMID:28533334
Characterisation of the nicotianamine aminotransferase and deoxymugineic acid synthase genes essential to Strategy II iron uptake in bread wheat (Triticum aestivum L.). PMID:28475636
Evolution of the 3R-MYB Gene Family in Plants. PMID:28444194
FcRav2, a gene with a ROGDI domain involved in Fusarium head blight and crown rot on durum wheat caused by Fusarium culmorum. PMID:28322011
Bioinformatics identification of new targets for improving low temperature stress tolerance in spring and winter wheat. PMID:28302069
Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation. PMID:27791104
Genome-Wide Analysis, Classification, Evolution, and Expression Analysis of the Cytochrome P450 93 Family in Land Plants. PMID:27760179
The Plant Cell Wall: A Complex and Dynamic Structure As Revealed by the Responses of Genes under Stress Conditions. PMID:27559336
Genome-wide characterization of soybean P 1B -ATPases gene family provides functional implications in cadmium responses. PMID:27207280
Black perithecial pigmentation in Fusarium species is due to the accumulation of 5-deoxybostrycoidin-based melanin. PMID:27193384
Identification and molecular characterization of the nicotianamine synthase gene family in bread wheat. PMID:27155533
Auxin and Cell Wall Invertase Related Signaling during Rice Grain Development. PMID:27135493
Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations. PMID:27129738
Genetic Diversity and Genome Wide Association Study of β-Glucan Content in Tetraploid Wheat Grains. PMID:27045166
Compartmentalized gene regulatory network of the pathogenic fungus Fusarium graminearum. PMID:26990214
Genome-wide identification and characterization of Glyceraldehyde-3-phosphate dehydrogenase genes family in wheat (Triticum aestivum). PMID:26984398
Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes. PMID:26956888
Evolution and Functional Insights of Different Ancestral Orthologous Clades of Chitin Synthase Genes in the Fungal Tree of Life. PMID:26870058
expVIP: a Customizable RNA-seq Data Analysis and Visualization Platform. PMID:26869702
Identification of Gene Modules Associated with Low Temperatures Response in Bambara Groundnut by Network-Based Analysis. PMID:26859686
A characterization of grapevine of GRAS domain transcription factor gene family. PMID:26842940
Comparative genome-wide transcriptome analysis of Vitis vinifera responses to adapted and non-adapted strains of two-spotted spider mite, Tetranyhus urticae. PMID:26801623
Bioinformatic landscapes for plant transcription factor system research. PMID:26719053
WheatExp: an RNA-seq expression database for polyploid wheat. PMID:26705106
Evolution, diversification, and expression of KNOX proteins in plants. PMID:26557129
New insights into the interplay between codon bias determinants in plants. PMID:26546225
Genome-Wide Comparative Analysis of Flowering-Related Genes in Arabidopsis, Wheat, and Barley. PMID:26435710
MaizeGDB update: new tools, data and interface for the maize model organism database. PMID:26432828
Translational genomics for plant breeding with the genome sequence explosion. PMID:26269219
Phylogenomics databases for facilitating functional genomics in rice. PMID:26223238
Comparative analysis of the phytocyanin gene family in 10 plant species: a focus on Zea mays. PMID:26217366
The knottin-like Blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions. PMID:26089830
Molecular and functional characterization of the durum wheat TdRL1, a member of the conserved Poaceae RSS1-like family that exhibits features of intrinsically disordered proteins and confers stress tolerance in yeast. PMID:26071212
Genome-Wide Analysis in Three Fusarium Pathogens Identifies Rapidly Evolving Chromosomes and Genes Associated with Pathogenicity. PMID:25994930
Endophytic colonization of barley (Hordeum vulgare) roots by the nematophagous fungus Pochonia chlamydosporia reveals plant growth promotion and a general defense and stress transcriptomic response. PMID:25982739
Conservation and divergence of the cyclic adenosine monophosphate-protein kinase A (cAMP-PKA) pathway in two plant-pathogenic fungi: Fusarium graminearum and F. verticillioides. PMID:25907134
Multiple elements controlling the expression of wheat high molecular weight glutenin paralogs. PMID:25893709
The barley powdery mildew candidate secreted effector protein CSEP0105 inhibits the chaperone activity of a small heat shock protein. PMID:25770154
Determining the subcellular location of synthesis and assembly of the cell wall polysaccharide (1,3; 1,4)-β-D-glucan in grasses. PMID:25770111
EXPath: a database of comparative expression analysis inferring metabolic pathways for plants. PMID:25708775
The naked endosperm genes encode duplicate INDETERMINATE domain transcription factors required for maize endosperm cell patterning and differentiation. PMID:25552497
Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. PMID:25534030
Structural and biochemical analysis of the Hordeum vulgare L. HvGR-RBP1 protein, a glycine-rich RNA-binding protein involved in the regulation of barley plant development and stress response. PMID:25495582
The grapevine gene nomenclature system. PMID:25481684
Identification and molecular characterization of tissue-preferred rice genes and their upstream regularly sequences on a genome-wide level. PMID:25428432
The Pathogen-Host Interactions database (PHI-base): additions and future developments. PMID:25414340
The Fusarium graminearum genome reveals more secondary metabolite gene clusters and hints of horizontal gene transfer. PMID:25333987
Inspection of the grapevine BURP superfamily highlights an expansion of RD22 genes with distinctive expression features in berry development and ABA-mediated stress responses. PMID:25330210
Dissecting the transcriptional response to elicitors in Vitis vinifera cells. PMID:25314001
Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. PMID:25261191
Interactions Among Plant Transcription Factors Regulating Expression of Stress-responsive Genes. PMID:25249757
A novel binary T-vector with the GFP reporter gene for promoter characterization. PMID:25197968
Discovering study-specific gene regulatory networks. PMID:25191999
Metabolic effects of elevated temperature on organic acid degradation in ripening Vitis vinifera fruit. PMID:25180109
RNAseq analysis of cassava reveals similar plant responses upon infection with pathogenic and non-pathogenic strains of Xanthomonas axonopodis pv. manihotis. PMID:25120000
Annotation of gene function in citrus using gene expression information and co-expression networks. PMID:25023870
Myb14, a direct activator of STS, is associated with resveratrol content variation in berry skin in two grape cultivars. PMID:24948530
Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera. PMID:24755338
Expression analysis of abscisic acid (ABA) and metabolic signalling factors in developing endosperm and embryo of barley. PMID:24748715
Species-specific expansion and molecular evolution of the 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) gene family in plants. PMID:24722776
Genome-wide identification, evolution and expression analysis of mTERF gene family in maize. PMID:24718683
Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene. PMID:24586171
Transcriptomic and proteomic analyses of a pale-green durum wheat mutant shows variations in photosystem components and metabolic deficiencies under drought stress. PMID:24521234
Genetic control of rhizomes and genomic localization of a major-effect growth habit QTL in perennial wildrye. PMID:24509730
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. PMID:24451627
Agrobacterium infection and plant defense-transformation success hangs by a thread. PMID:24391655
VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine). PMID:24341535
Description of durum wheat linkage map and comparative sequence analysis of wheat mapped DArT markers with rice and Brachypodium genomes. PMID:24304553
The Rice Oligonucleotide Array Database: an atlas of rice gene expression. PMID:24279809
Different stress responsive strategies to drought and heat in two durum wheat cultivars with contrasting water use efficiency. PMID:24267539
Transcriptome analysis of heat stress response in switchgrass (Panicum virgatum L.). PMID:24093800
Perturbation of Brachypodium distachyon CELLULOSE SYNTHASE A4 or 7 results in abnormal cell walls. PMID:24024469
Construction of a rice glycoside hydrolase phylogenomic database and identification of targets for biofuel research. PMID:23986771
LIFEGUARD proteins support plant colonization by biotrophic powdery mildew fungi. PMID:23888068
eFG: an electronic resource for Fusarium graminearum. PMID:23798489
Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization. PMID:23777981
A component of the Sec61 ER protein transporting pore is required for plant susceptibility to powdery mildew. PMID:23720664
Phytochrome-interacting factors have both shared and distinct biological roles. PMID:23708772
Genome-wide identification and evolutionary and expression analyses of MYB-related genes in land plants. PMID:23690543
Prospects for advancing defense to cereal rusts through genetical genomics. PMID:23641250
Computational predictions provide insights into the biology of TAL effector target sites. PMID:23526890
Reverse engineering: a key component of systems biology to unravel global abiotic stress cross-talk. PMID:23293646
Reuse of public genome-wide gene expression data. PMID:23269463
In planta stage-specific fungal gene profiling elucidates the molecular strategies of Fusarium graminearum growing inside wheat coleoptiles. PMID:23266949
Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression. PMID:23227855
RiceFREND: a platform for retrieving coexpressed gene networks in rice. PMID:23180784
RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. PMID:23180765
PICARA, an analytical pipeline providing probabilistic inference about a priori candidates genes underlying genome-wide association QTL in plants. PMID:23144785
Transcriptome variation along bud development in grapevine (Vitis vinifera L.). PMID:23035802
Poplar wood rays are involved in seasonal remodeling of tree physiology. PMID:22992511
Comprehensive analysis of NAC domain transcription factor gene family in Vitis vinifera. PMID:22983198
A comparative analysis of proteins that accumulate during the initial stage of root hair development in barley root hair mutants and their parent varieties. PMID:22847350
Transcriptional and metabolic analysis of senescence induced by preventing pollination in maize. PMID:22732243
The Wor1-like protein Fgp1 regulates pathogenicity, toxin synthesis and reproduction in the phytopathogenic fungus Fusarium graminearum. PMID:22693448
Metabolome and transcriptome of the interaction between Ustilago maydis and Fusarium verticillioides in vitro. PMID:22407693
BarleyBase/PLEXdb PubMed citations: 41.

41 articles citing: BarleyBase/PLEXdb

Robust gene selection methods using weighting schemes for microarray data analysis. PMID:28865426
Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition. PMID:25596183
Genome-wide identification, characterization and expression analysis of the auxin response factor gene family in Vitis vinifera. PMID:24792421
The basic leucine zipper transcription factor ABSCISIC ACID RESPONSE ELEMENT-BINDING FACTOR2 is an important transcriptional regulator of abscisic acid-dependent grape berry ripening processes. PMID:24276949
Different stress responsive strategies to drought and heat in two durum wheat cultivars with contrasting water use efficiency. PMID:24267539
Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum. PMID:23861834
Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum. PMID:23805903
eFG: an electronic resource for Fusarium graminearum. PMID:23798489
Genomic organization, phylogenetic comparison and differential expression of the SBP-box family genes in grape. PMID:23527172
Endo-(1,4)-β-glucanase gene families in the grasses: temporal and spatial co-transcription of orthologous genes. PMID:23231659
Genome-wide identification and analysis of the TIFY gene family in grape. PMID:22984514
Bioinformatics opportunities for identification and study of medicinal plants. PMID:22589384
Poplar extrafloral nectaries: two types, two strategies of indirect defenses against herbivores. PMID:22573802
ArraySearch: A Web-Based Genomic Search Engine. PMID:22474412
Barley ROP binding kinase1 is involved in microtubule organization and in basal penetration resistance to the barley powdery mildew fungus. PMID:22415513
Genome-wide identification and analysis of grape aldehyde dehydrogenase (ALDH) gene superfamily. PMID:22355416
POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data. PMID:22253616
The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes. PMID:22120664
OmniMapFree: a unified tool to visualise and explore sequenced genomes. PMID:22085540
PLEXdb: gene expression resources for plants and plant pathogens. PMID:22084198
PlantRGS: a web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants. PMID:21987088
Analyses of the oligopeptide transporter gene family in poplar and grape. PMID:21943393
The Vitis vinifera C-repeat binding protein 4 (VvCBF4) transcriptional factor enhances freezing tolerance in wine grape. PMID:21914113
Soybean homologs of MPK4 negatively regulate defense responses and positively regulate growth and development. PMID:21878550
Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation. PMID:21791600
MaizeGDB: curation and outreach go hand-in-hand. PMID:21624896
Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. PMID:21441235
B2G-FAR, a species-centered GO annotation repository. PMID:21335611
Habituation to thaxtomin A in hybrid poplar cell suspensions provides enhanced and durable resistance to inhibitors of cellulose synthesis. PMID:21143977
FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum. PMID:21051345
MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. PMID:20958970
Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. PMID:20539294
Systematic discovery of regulatory motifs in Fusarium graminearum by comparing four Fusarium genomes. PMID:20346147
Transcriptomic analysis of starch biosynthesis in the developing grain of hexaploid wheat. PMID:20224818
Complementary genetic and genomic approaches help characterize the linkage group I seed protein QTL in soybean. PMID:20199683
VitisNet: "Omics" integration through grapevine molecular networks. PMID:20027228
Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array. PMID:19480707
TRUNCATULIX--a data warehouse for the legume community. PMID:19210766
The international barley sequencing consortium--at the threshold of efficient access to the barley genome. PMID:19126706
Regulon organization of Arabidopsis. PMID:18826618
SoyXpress: a database for exploring the soybean transcriptome. PMID:18671881
http://dx.doi.org/10.1093/nar/GKR938

Tags:

Tags
More detailed information about this field from each metasource.

deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: PLEXdb; PLEXdb; DOI: https://doi.org/10.25504/FAIRsharing.8pjgwx; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

gene
metasource: Fairsharing.org
version: FAIRsharing.org: PLEXdb; PLEXdb; DOI: https://doi.org/10.25504/FAIRsharing.8pjgwx; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: PLEXdb; PLEXdb; DOI: https://doi.org/10.25504/FAIRsharing.8pjgwx; Last edited: Jan. 8, 2019, 1:14 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

general plant databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

biology
metasource: re3data.org
version: re3data.org: PLEXdb; editing status 2019-08-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R39D13 last accessed: 2022-11-04

expression profiling
metasource: re3data.org
version: re3data.org: PLEXdb; editing status 2019-08-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R39D13 last accessed: 2022-11-04

genetics
metasource: re3data.org
version: re3data.org: PLEXdb; editing status 2019-08-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R39D13 last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: PLEXdb; editing status 2019-08-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R39D13 last accessed: 2022-11-04

genotype
metasource: re3data.org
version: re3data.org: PLEXdb; editing status 2019-08-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R39D13 last accessed: 2022-11-04

pathway
metasource: re3data.org
version: re3data.org: PLEXdb; editing status 2019-08-08; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R39D13 last accessed: 2022-11-04

plant biology
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798

gene expression
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798

gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798

genotype and phenotype
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:16.605798

dna gene gene expression plant plant expression profiling genetics genomics genotype pathway plant biology model organisms gene expression gene transcripts genotype and phenotype

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