Arabidopsis Information Portal

Names
More detailed information about this field from each metasource.

Arabidopsis Information Portal
metasource: Fairsharing.org
version: None

Araport
metasource: Fairsharing.org
version: None

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

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:17.388699

araport
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:17.388699

Other names: Araport, araport

The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation including gene structure, gene expression, protein function, and interaction networks. Araport offers gene and protein reports with orthology, expression, interactions and the latest annotation, plus analysis tools, community apps, and web services. Araport is free and open-source. Registered members can save their analysis, publish science apps, and post announcements.

Webpage:

https://www.araport.org/

Licence:

Name: GNU General Public License (GPL) 3.0
URL: https://www.gnu.org/licenses/gpl.html

Publications:

Publications
More detailed information about this field from each metasource.

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome
PMID: 27862469
metasource: Fairsharing.org
version: None

metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:17.388699

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery
PMID: 28013278
metasource: Fairsharing.org
version: None

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

Araport11: a complete reannotation of the Arabidopsis thaliana reference genome PubMed citations: 302.

302 articles citing: Araport11: a complete reannotation of the Arabidopsis thaliana reference genome

Divergent evolution of extreme production of variant plant monounsaturated fatty acids. PMID:35867834
Seed Transmission of Pathogens: Non-Canonical Immune Response in Arabidopsis Germinating Seeds Compared to Early Seedlings against the Necrotrophic Fungus Alternaria brassicicola. PMID:35807659
A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. PMID:35799267
Identification of Candidate Genes for a Major Quantitative Disease Resistance Locus From Soybean PI 427105B for Resistance to Phytophthora sojae. PMID:35774827
Mining of Cloned Disease Resistance Gene Homologs (CDRHs) in Brassica Species and Arabidopsis thaliana. PMID:35741342
Transcriptomic Analysis Reveals LncRNAs Associated with Flowering of Angelica sinensis during Vernalization. PMID:35678657
Genome evolution and diversity of wild and cultivated potatoes. PMID:35676481
Recurrent Plant-Specific Duplications of KNL2 and Its Conserved Function as a Kinetochore Assembly Factor. PMID:35671323
Whole Genome Re-sequencing and Bulk Segregant Analysis Reveals Chromosomal Location for Papaya Ringspot Virus W Resistance in Squash. PMID:35665151
Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. PMID:35640880
A 3D gene expression atlas of the floral meristem based on spatial reconstruction of single nucleus RNA sequencing data. PMID:35595749
Genome-Wide Identification of Wild Soybean Mitochondrial Calcium Uniporter Family Genes and Their Responses to Cold and Carbonate Alkaline Stresses. PMID:35592573
Exploring Posttranslational Modifications with the Plant PTM Viewer. PMID:35583790
Enzymes degraded under high light maintain proteostasis by transcriptional regulation in Arabidopsis. PMID:35549553
Large-scale discovery of non-conventional peptides in grape (Vitis vinifera L.) through peptidogenomics. PMID:35531313
Root-Knot Nematode Resistance in Gossypium hirsutum Determined by a Constitutive Defense-Response Transcriptional Program Avoiding a Fitness Penalty. PMID:35498643
A target Capture Probe Set Useful for Deep- and Shallow-Level Phylogenetic Studies in Cactaceae. PMID:35456513
RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data. PMID:35443610
Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses. PMID:35443608
Global Patterns of Subgenome Evolution in Organelle-Targeted Genes of Six Allotetraploid Angiosperms. PMID:35383845
Molecular and physiological responses to desiccation indicate the abscisic acid pathway is conserved in the peat moss, Sphagnum. PMID:35383351
Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing. PMID:35371168
Automatic identification and annotation of MYB gene family members in plants. PMID:35305581
Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits. PMID:35283936
TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets. PMID:35243369
Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits. PMID:35212360
iLoci: robust evaluation of genome content and organization for provisional and mature genome assemblies. PMID:35211671
Changes in Gene Expression in Leaves of Cacao Genotypes Resistant and Susceptible to Phytophthora palmivora Infection. PMID:35211126
A New Approach Using Targeted Sequence Capture for Phylogenomic Studies across Cactaceae. PMID:35205394
Genomic variation reveals demographic history and biological adaptation of the ancient relictual, lotus (Nelumbo Adans). PMID:35184169
Genetic architecture of variation in Arabidopsis thaliana rosettes. PMID:35171969
An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development. PMID:35139889
Arabidopsis TBP-ASSOCIATED FACTOR 12 ortholog NOBIRO6 controls root elongation with unfolded protein response cofactor activity. PMID:35115407
NetSeekR: a network analysis pipeline for RNA-Seq time series data. PMID:35090393
Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana. PMID:35087200
A comparative genomics examination of desiccation tolerance and sensitivity in two sister grass species. PMID:35082155
Long Non-Coding RNAs as Emerging Regulators of Pathogen Response in Plants. PMID:35076574
To New Beginnings: Riboproteogenomics Discovery of N-Terminal Proteoforms in Arabidopsis Thaliana. PMID:35069635
Improved High-Quality Genome Assembly and Annotation of Pineapple (Ananas comosus) Cultivar MD2 Revealed Extensive Haplotype Diversity and Diversified FRS/FRF Gene Family. PMID:35052394
GWAS on multiple traits identifies mitochondrial ACONITASE3 as important for acclimation to submergence stress. PMID:35043967
Construction of integrative transcriptome to boost systematic exploration of Bougainvillea. PMID:35042937
Genome-wide identification and characterization of the CLASP_N gene family in upland cotton (Gossypium hirsutum L.). PMID:35036102
The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis. PMID:35027454
The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis. PMID:35017514
Genome-wide identification and expression analysis of the coronatine-insensitive 1 (COI1) gene family in response to biotic and abiotic stresses in Saccharum. PMID:34998383
Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum. PMID:34983397
Genome-Wide Identification and Expression Analysis of the Plant U-Box Protein Gene Family in Phyllostachys edulis. PMID:34917124
A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana. PMID:34906086
Two galacturonosyltransferases function in plant growth, stomatal development, and dynamics. PMID:34890462
Dissection of Quantitative Blackleg Resistance Reveals Novel Variants of Resistance Gene Rlm9 in Elite Brassica napus. PMID:34868134
Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. PMID:34850679
Shoot and root single cell sequencing reveals tissue- and daytime-specific transcriptome profiles. PMID:34850215
A Decade of Pollen Phosphoproteomics. PMID:34830092
Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing. PMID:34823554
Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution. PMID:34820204
Genes involved in mRNA surveillance are induced in Brachypodium distachyon under cadmium toxicity. PMID:34812999
High rates of evolution preceded shifts to sex-biased gene expression in Leucadendron, the most sexually dimorphic angiosperms. PMID:34726596
Characterization of the Brassica napus Flavonol Synthase Gene Family Reveals Bifunctional Flavonol Synthases. PMID:34721462
Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots. PMID:34685382
A consensus-based ensemble approach to improve transcriptome assembly. PMID:34674629
The genome-wide rate and spectrum of EMS-induced heritable mutations in the microcrustacean Daphnia: on the prospect of forward genetics. PMID:34667306
Large structural variations in the haplotype-resolved African cassava genome. PMID:34661327
Three chromosome-scale Papaver genomes reveal punctuated patchwork evolution of the morphinan and noscapine biosynthesis pathway. PMID:34654815
Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning. PMID:34645826
A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum. PMID:34620992
Long-term acclimation to cadmium exposure reveals extensive phenotypic plasticity in Chlamydomonas. PMID:34618070
Atypical molecular features of RNA silencing against the phloem-restricted polerovirus TuYV. PMID:34614168
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. PMID:34591957
Principles of mRNA targeting via the Arabidopsis m6A-binding protein ECT2. PMID:34591015
Evolutionarily informed machine learning enhances the power of predictive gene-to-phenotype relationships. PMID:34561450
Genomic impact of stress-induced transposable element mobility in Arabidopsis. PMID:34551439
Dual transcriptomic analysis reveals metabolic changes associated with differential persistence of human pathogenic bacteria in leaves of Arabidopsis and lettuce. PMID:34550367
Genome-wide Excision Repair Map of Cyclobutane Pyrimidine Dimers in Arabidopsis and the Roles of CSA1 and CSA2 Proteins in Transcription-coupled Repair. PMID:34525225
The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases. PMID:34465729
The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. PMID:34411258
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
Large scale genomic rearrangements in selected Arabidopsis thaliana T-DNA lines are caused by T-DNA insertion mutagenesis. PMID:34362298
The RGF/GLV/CLEL Family of Short Peptides Evolved Through Lineage-Specific Losses and Diversification and Yet Conserves Its Signaling Role Between Vascular Plants and Bryophytes. PMID:34354727
FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing. PMID:34331052
Genome-wide analysis of butterfly bush (Buddleja alternifolia) in three uplands provides insights into biogeography, demography and speciation. PMID:34292587
Genome-Wide Comparative Analysis of Flowering-Time Genes; Insights on the Gene Family Expansion and Evolutionary Perspective. PMID:34290729
The DUB family in Populus: identification, characterization, evolution and expression patterns. PMID:34266381
Identification of Small RNAs During High Light Acclimation in Arabidopsis thaliana. PMID:34211484
Effects of the Developmental Regulator BOLITA on the Plant Metabolome. PMID:34209960
Arabidopsis thaliana Myb59 Gene Is Involved in the Response to Heterodera schachtii Infestation, and Its Overexpression Disturbs Regular Development of Nematode-Induced Syncytia. PMID:34208611
Whole-Genome Duplication Facilitated the Evolution of C4 Photosynthesis in Gynandropsis gynandra. PMID:34191030
Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts. PMID:34143496
Gene expression variation in Arabidopsis embryos at single-nucleus resolution. PMID:34142712
Synthetic promoter designs enabled by a comprehensive analysis of plant core promoters. PMID:34083762
Molecular Targets and Biological Functions of cAMP Signaling in Arabidopsis. PMID:34063698
Transcriptional and imprinting complexity in Arabidopsis seeds at single-nucleus resolution. PMID:34059805
TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes. PMID:34058980
Genome-wide identification of the DUF668 gene family in cotton and expression profiling analysis of GhDUF668 in Gossypium hirsutum under adverse stress. PMID:34044774
Genome-wide DNA mutations in Arabidopsis plants after multigenerational exposure to high temperatures. PMID:34034794
The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation. PMID:33976212
Shedding Light on the Dynamic Role of the "Target of Rapamycin" Kinase in the Fast-Growing C4 Species Setaria viridis, a Suitable Model for Biomass Crops. PMID:33927734
Characterization of the Survival Influential Genes in Carcinogenesis. PMID:33922264
Characterization of the ERP gene family in Arabidopsis thaliana. PMID:33906568
Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. PMID:33904405
Normal, novel or none: versatile regulation from alternative splicing. PMID:33882794
FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences. PMID:33879057
The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible. PMID:33863805
Metatranscriptomic Comparison of Endophytic and Pathogenic Fusarium-Arabidopsis Interactions Reveals Plant Transcriptional Plasticity. PMID:33856230
The molecular signatures of compatible and incompatible pollination in Arabidopsis. PMID:33853522
Label-Free Quantitative Proteomic Analysis of Nitrogen Starvation in Arabidopsis Root Reveals New Aspects of H2S Signaling by Protein Persulfidation. PMID:33805243
The nucleolar protein SAHY1 is involved in pre-rRNA processing and normal plant growth. PMID:33793900
Anno genominis XX: 20 years of Arabidopsis genomics. PMID:33793861
Profiling of RNA ribose methylation in Arabidopsis thaliana. PMID:33784398
Genomic editing of intronic enhancers unveils their role in fine-tuning tissue-specific gene expression in Arabidopsis thaliana. PMID:33764459
Meiocyte Isolation by INTACT and Meiotic Transcriptome Analysis in Arabidopsis. PMID:33747019
Comparative transcriptomic analysis of thermally stressed Arabidopsis thaliana meiotic recombination mutants. PMID:33711924
Functional and evolutionary analysis of the Arabidopsis 4R-MYB protein SNAPc4 as part of the SNAP complex. PMID:33693812
The Mitragyna speciosa (Kratom) Genome: a resource for data-mining potent pharmaceuticals that impact human health. PMID:33677570
Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum. PMID:33643360
Reannotation of the cultivated strawberry genome and establishment of a strawberry genome database. PMID:33642572
RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars 'TAM 111' and 'TAM 112'. PMID:33619336
Dynamic histone acetylation in floral volatile synthesis and emission in petunia flowers. PMID:33606881
Prioritization and Evaluation of Flooding Tolerance Genes in Soybean [Glycine max (L.) Merr.]. PMID:33584812
Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures. PMID:33582756
A Pipeline towards the Biochemical Characterization of the Arabidopsis GT14 Family. PMID:33572987
Priming with a Seaweed Extract Strongly Improves Drought Tolerance in Arabidopsis. PMID:33540571
Physiological and Proteomic Signatures Reveal Mechanisms of Superior Drought Resilience in Pearl Millet Compared to Wheat. PMID:33519854
LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate. PMID:33504790
Phototropin 1 and 2 Influence Photosynthesis, UV-C Induced Photooxidative Stress Responses, and Cell Death. PMID:33498294
Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana. PMID:33459869
Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals. PMID:33446251
Genome-wide identification and analysis of DNA methyltransferase and demethylase gene families in Dendrobium officinale reveal their potential functions in polysaccharide accumulation. PMID:33407149
Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing. PMID:33406240
Recent Findings Unravel Genes and Genetic Factors Underlying Leptosphaeria maculans Resistance in Brassica napus and Its Relatives. PMID:33396785
Insight into early diversification of leucine-rich repeat receptor-like kinases provided by the sequenced moss and hornwort genomes. PMID:33389562
Cytokinin isopentenyladenine and its glucoside isopentenyladenine-9G delay leaf senescence through activation of cytokinin-associated genes. PMID:33364544
Identification of Cis-Regulatory Sequences Controlling Pollen-Specific Expression of Hydroxyproline-Rich Glycoprotein Genes in Arabidopsis thaliana. PMID:33322028
EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome. PMID:33245626
Expression Partitioning of Duplicate Genes at Single Cell Resolution in Arabidopsis Roots. PMID:33240334
Identification and Characterization of the Heat-Induced Plastidial Stress Granules Reveal New Insight Into Arabidopsis Stress Response. PMID:33224174
Large-Scale Phosphoproteomic Study of Arabidopsis Membrane Proteins Reveals Early Signaling Events in Response to Cold. PMID:33207747
RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile. PMID:33198137
Adaptive Evolution of Chalcone Isomerase Superfamily in Fagaceae. PMID:33135088
Application of Genomic Big Data in Plant Breeding:Past, Present, and Future. PMID:33126607
Reference transcriptomes and comparative analyses of six species in the threatened rosewood genus Dalbergia. PMID:33082403
Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation. PMID:33054972
TERMINAL FLOWER 1-FD complex target genes and competition with FLOWERING LOCUS T. PMID:33046692
Proteomic and transcriptomic profiling of aerial organ development in Arabidopsis. PMID:33037224
The Arabidopsis RLCK VI_A2 Kinase Controls Seedling and Plant Growth in Parallel with Gibberellin. PMID:33019674
Database: web application for visualization of the cumulated RNAseq data against the salicylic acid (SA) and methyl jasmonate (MeJA) treatment of Arabidopsis thaliana. PMID:33008298
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Genome-wide identification and expression patterns analysis of the RPD3/HDA1 gene family in cotton. PMID:32948145
Generation of a chromosome-scale genome assembly of the insect-repellent terpenoid-producing Lamiaceae species, Callicarpa americana. PMID:32893861
Seasonal plasticity and diel stability of H3K27me3 in natural fluctuating environments. PMID:32868888
Uclacyanin Proteins Are Required for Lignified Nanodomain Formation within Casparian Strips. PMID:32857976
Arabinoxylan-Oligosaccharides Act as Damage Associated Molecular Patterns in Plants Regulating Disease Resistance. PMID:32849751
Novel Role of JAC1 in Influencing Photosynthesis, Stomatal Conductance, and Photooxidative Stress Signalling Pathway in Arabidopsis thaliana. PMID:32849690
Resistance Gene Analogs in the Brassicaceae: Identification, Characterization, Distribution, and Evolution. PMID:32796089
A single-population GWAS identified AtMATE expression level polymorphism caused by promoter variants is associated with variation in aluminum tolerance in a local Arabidopsis population. PMID:32793853
Global Role of Crop Genomics in the Face of Climate Change. PMID:32765541
Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae. PMID:32735328
Phylogenomic proof of Recurrent Demipolyploidization and Evolutionary Stalling of the "Triploid Bridge" in Arundo (Poaceae). PMID:32722033
Araport Lives: An Updated Framework for Arabidopsis Bioinformatics. PMID:32699173
IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. PMID:32683045
Cell type-specific genome scans of DNA methylation divergence indicate an important role for transposable elements. PMID:32660534
New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs. PMID:32652016
VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development. PMID:32646368
Genome assembly of Chiococca alba uncovers key enzymes involved in the biosynthesis of unusual terpenoids. PMID:32642754
Active DNA demethylation regulates tracheary element differentiation in Arabidopsis. PMID:32637594
The Intrinsically Disordered Protein CARP9 Bridges HYL1 to AGO1 in the Nucleus to Promote MicroRNA Activity. PMID:32636339
Cross-Species Annotation of Expressed Genes and Detection of Different Functional Gene Modules Between 10 Cold- and 10 Hot-Propertied Chinese Herbal Medicines. PMID:32625232
Extensive signal integration by the phytohormone protein network. PMID:32612234
Identification of small RNAs during cold acclimation in Arabidopsis thaliana. PMID:32600430
Centralization Within Sub-Experiments Enhances the Biological Relevance of Gene Co-expression Networks: A Plant Mitochondrial Case Study. PMID:32582224
Splice2Deep: An ensemble of deep convolutional neural networks for improved splice site prediction in genomic DNA. PMID:32550561
Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants. PMID:32541953
Synergy between the anthocyanin and RDR6/SGS3/DCL4 siRNA pathways expose hidden features of Arabidopsis carbon metabolism. PMID:32415123
Nutrient dose-responsive transcriptome changes driven by Michaelis-Menten kinetics underlie plant growth rates. PMID:32414922
Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation. PMID:32404413
Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis. PMID:32312999
Identifying genetic variants underlying phenotypic variation in plants without complete genomes. PMID:32284578
Functional Features of TREHALOSE-6-PHOSPHATE SYNTHASE1, an Essential Enzyme in Arabidopsis. PMID:32276986
AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. PMID:32265262
Splicing conservation signals in plant long noncoding RNAs. PMID:32241834
High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PMID:32236090
Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways. PMID:32213639
Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin. PMID:32205451
Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress. PMID:32193425
Evolutionary History and Activity of RNase H1-Like Proteins in Arabidopsis thaliana. PMID:32191307
High Contiguity De Novo Genome Sequence Assembly of Trifoliate Yam (Dioscorea dumetorum) Using Long Read Sequencing. PMID:32143301
A plant-specific SWR1 chromatin-remodeling complex couples histone H2A.Z deposition with nucleosome sliding. PMID:32115743
A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs. PMID:32082334
Chromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics. PMID:32080174
Natural variation in DNA methylation homeostasis and the emergence of epialleles. PMID:32071208
TOR dynamically regulates plant cell-cell transport. PMID:32051250
A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening. PMID:31992236
Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant (Camellia sinensis) under abiotic stress and withering processing. PMID:31976183
A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress. PMID:31940839
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification. PMID:31931956
Plant metabolism of nematode pheromones mediates plant-nematode interactions. PMID:31924834
RNA-seq, de novo transcriptome assembly and flavonoid gene analysis in 13 wild and cultivated berry fruit species with high content of phenolics. PMID:31856735
Direct comparison of Arabidopsis gene expression reveals different responses to melatonin versus auxin. PMID:31856719
Compensatory sequence variation between trans-species small RNAs and their target sites. PMID:31845648
An Online Database for Exploring Over 2,000 Arabidopsis Small RNA Libraries. PMID:31843802
Dormancy cycling: translation-related transcripts are the main difference between dormant and non-dormant seeds in the field. PMID:31785171
An N-terminal motif in NLR immune receptors is functionally conserved across distantly related plant species. PMID:31774397
Targeted misexpression of NAC052, acting in H3K4 demethylation, alters leaf morphological and anatomical traits in Arabidopsis thaliana. PMID:31740936
Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand's high ultraviolet B radiation environment. PMID:31718535
Expression Atlas update: from tissues to single cells. PMID:31665515
The Trithorax Group Factor ULTRAPETALA1 Regulates Developmental as Well as Biotic and Abiotic Stress Response Genes in Arabidopsis. PMID:31604825
Selecting Closely-Linked SNPs Based on Local Epistatic Effects for Haplotype Construction Improves Power of Association Mapping. PMID:31604824
Genome-Wide Identification of WRKY Transcription Factors in the Asteranae. PMID:31581604
PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding. PMID:31551361
Integrative Analysis from the Epigenome to Translatome Uncovers Patterns of Dominant Nuclear Regulation during Transient Stress. PMID:31519798
Protein phosphatase 2A regulates the nuclear accumulation of the Arabidopsis bZIP protein VIP1 under hypo-osmotic stress. PMID:31504762
Construction of pseudomolecule sequences of Brassica rapa ssp. pekinensis inbred line CT001 and analysis of spontaneous mutations derived via sexual propagation. PMID:31498838
Excess Light Priming in Arabidopsis thaliana Genotypes with Altered DNA Methylomes. PMID:31484672
A Species-Wide Inventory of NLR Genes and Alleles in Arabidopsis thaliana. PMID:31442410
Plant Defenses Against Pests Driven by a Bidirectional Promoter. PMID:31379907
Accelerating structure-function mapping using the ViVa webtool to mine natural variation. PMID:31372596
An 'eFP-Seq Browser' for visualizing and exploring RNA sequencing data. PMID:31350781
Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions. PMID:31331261
Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants. PMID:31316532
De novo genome assembly of the endangered Acer yangbiense, a plant species with extremely small populations endemic to Yunnan Province, China. PMID:31307060
SPX4 Acts on PHR1-Dependent and -Independent Regulation of Shoot Phosphorus Status in Arabidopsis. PMID:31262954
A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana. PMID:31250033
Many rice genes are differentially spliced between roots and shoots but cytokinin has minimal effect on splicing. PMID:31245776
Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships. PMID:31235560
Sulfated plant peptide hormones. PMID:31231771
A Series of Fortunate Events: Introducing Chlamydomonas as a Reference Organism. PMID:31189738
ANASTASIA: An Automated Metagenomic Analysis Pipeline for Novel Enzyme Discovery Exploiting Next Generation Sequencing Data. PMID:31178894
Bridging the gap between reference and real transcriptomes. PMID:31159855
Generic Repeat Finder: A High-Sensitivity Tool for Genome-Wide De Novo Repeat Detection. PMID:31152127
Arabidopsis DGD1 SUPPRESSOR1 Is a Subunit of the Mitochondrial Contact Site and Cristae Organizing System and Affects Mitochondrial Biogenesis. PMID:31118221
Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination. PMID:31113491
A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set. PMID:31112551
Updated annotation of the wild strawberry Fragaria vesca V4 genome. PMID:31069085
Lasy-Seq: a high-throughput library preparation method for RNA-Seq and its application in the analysis of plant responses to fluctuating temperatures. PMID:31068632
Identification of Transcription Factors Regulating Senescence in Wheat through Gene Regulatory Network Modelling. PMID:31064813
CEP-CEPR1 signalling inhibits the sucrose-dependent enhancement of lateral root growth. PMID:31056646
An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK! PMID:30945176
A quick guide for student-driven community genome annotation. PMID:30943207
Tasselseed5 overexpresses a wound-inducible enzyme, ZmCYP94B1, that affects jasmonate catabolism, sex determination, and plant architecture in maize. PMID:30937397
Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters. PMID:30908494
ANAC017 Coordinates Organellar Functions and Stress Responses by Reprogramming Retrograde Signaling. PMID:30872424
Multispecies genome-wide analysis defines the MAP3K gene family in Gossypium hirsutum and reveals conserved family expansions. PMID:30871456
Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs. PMID:30760640
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. PMID:30689848
Proteome-wide, Structure-Based Prediction of Protein-Protein Interactions/New Molecular Interactions Viewer. PMID:30679268
Transcriptomics of Arabidopsis sperm cells at single-cell resolution. PMID:30675644
Extracellular ATP Shapes a Defense-Related Transcriptome Both Independently and along with Other Defense Signaling Pathways. PMID:30630869
The embryonic transcriptome of Arabidopsis thaliana. PMID:30610360
A Phytophthora Effector Suppresses Trans-Kingdom RNAi to Promote Disease Susceptibility. PMID:30595554
Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes. PMID:30594132
High-throughput sequencing data and the impact of plant gene annotation quality. PMID:30590678
A Golgi-Released Subpopulation of the Trans-Golgi Network Mediates Protein Secretion in Arabidopsis. PMID:30545905
Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators. PMID:30500810
Landscape of gene transposition-duplication within the Brassicaceae family. PMID:30380026
Arabidopsis RIBOSOMAL RNA PROCESSING7 Is Required for 18S rRNA Maturation. PMID:30361235
Early Responses to Severe Drought Stress in the Arabidopsis thaliana Cell Suspension Culture Proteome. PMID:30279377
A Two-Headed Monster to Avert Disaster: HBS1/SKI7 Is Alternatively Spliced to Build Eukaryotic RNA Surveillance Complexes. PMID:30258456
A major QTL on chromosome C05 significantly reduces acid detergent lignin (ADL) content and increases seed oil and protein content in oilseed rape (Brassica napus L.). PMID:30143828
A comparison of heat-stress transcriptome changes between wild-type Arabidopsis pollen and a heat-sensitive mutant harboring a knockout of cyclic nucleotide-gated cation channel 16 (cngc16). PMID:30041596
High Quality de Novo Transcriptome Assembly of Croton tiglium. PMID:30027092
Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana. PMID:29970452
HEAT INDUCIBLE LIPASE1 Remodels Chloroplastic Monogalactosyldiacylglycerol by Liberating α-Linolenic Acid in Arabidopsis Leaves under Heat Stress. PMID:29967047
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant. PMID:29931210
Arabidopsis response to the spider mite Tetranychus urticae depends on the regulation of reactive oxygen species homeostasis. PMID:29930298
INCURVATA11 and CUPULIFORMIS2 Are Redundant Genes That Encode Epigenetic Machinery Components in Arabidopsis. PMID:29915151
Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize. PMID:29879919
The Chromatin Remodelers PKL and PIE1 Act in an Epigenetic Pathway That Determines H3K27me3 Homeostasis in Arabidopsis. PMID:29802212
An improved assembly and annotation of the melon (Cucumis melo L.) reference genome. PMID:29795526
A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing. PMID:29712755
Predicting gene structure changes resulting from genetic variants via exon definition features. PMID:29701825
Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions. PMID:29697803
Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map. PMID:29679055
A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants. PMID:29661190
An m6A-YTH Module Controls Developmental Timing and Morphogenesis in Arabidopsis. PMID:29643069
Biology in Bloom: A Primer on the Arabidopsis thaliana Model System. PMID:29618591
Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions. PMID:29530928
A Newly Identified Flower-Specific Splice Variant of AUXIN RESPONSE FACTOR8 Regulates Stamen Elongation and Endothecium Lignification in Arabidopsis. PMID:29514943
Different Modes of Negative Regulation of Plant Immunity by Calmodulin-Related Genes. PMID:29449432
Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome. PMID:29440596
High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell. PMID:29416032
ER-Anchored Transcription Factors bZIP17 and bZIP28 Regulate Root Elongation. PMID:29367234
Genome-Wide Analysis of the Arabidopsis Replication Timing Program. PMID:29301956
Elongated Hypocotyl 5-Homolog (HYH) Negatively Regulates Expression of the Ambient Temperature-Responsive MicroRNA Gene MIR169. PMID:29270188
Inferring defense-related gene families in Arabidopsis and wheat. PMID:29258426
Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds. PMID:29250090
Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. PMID:29202864
Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits. PMID:29149280
Annotating and quantifying pri-miRNA transcripts using RNA-Seq data of wild type and serrate-1 globular stage embryos of Arabidopsis thaliana. PMID:29124087
Divergence and Conservative Evolution of XTNX Genes in Land Plants. PMID:29123540
Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation. PMID:29087317
Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets. PMID:29036429
The Arabidopsis DNA Methylome Is Stable under Transgenerational Drought Stress. PMID:28986422
Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PMID:28902852
Evolutionarily Conserved Alternative Splicing Across Monocots. PMID:28839042
Long Noncoding RNAs in Plants. PMID:28815539
A plant effector-triggered immunity signaling sector is inhibited by pattern-triggered immunity. PMID:28811287
Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data. PMID:28724941
Analysis of CFB, a cytokinin-responsive gene of Arabidopsis thaliana encoding a novel F-box protein regulating sterol biosynthesis. PMID:28505379
Proximal methylation features associated with nonrandom changes in gene body methylation. PMID:28446217
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. PMID:28402429
Widespread Contamination of Arabidopsis Embryo and Endosperm Transcriptome Data Sets. PMID:28314828
Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation. PMID:28013277
A Cysteine-Rich Protein Kinase Associates with a Membrane Immune Complex and the Cysteine Residues Are Required for Cell Death. PMID:27852951
ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery PubMed citations: 13.

13 articles citing: ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery

HumanMine: advanced data searching, analysis and cross-species comparison. PMID:35820040
Regulation of heat shock proteins 70 and their role in plant immunity. PMID:35022724
Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species. PMID:33676571
Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana. PMID:33459869
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
Regulation of ribosomal protein genes: An ordered anarchy. PMID:33038057
PartCrafter: find, generate and analyze BioParts. PMID:32995539
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
Root Skewing-Associated Genes Impact the Spaceflight Response of Arabidopsis thaliana. PMID:32194611
Structural evolution drives diversification of the large LRR-RLK gene family. PMID:31990988
Shaping Ethylene Response: The Role of EIN3/EIL1 Transcription Factors. PMID:31507622
Overexpression of Acyl-ACP Thioesterases, CpFatB4 and CpFatB5, Induce Distinct Gene Expression Reprogramming in Developing Seeds of Brassica napus. PMID:31284614
Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions. PMID:30111865
http://dx.doi.org/10.1093/nar/

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gene expression
metasource: Fairsharing.org
version: None

gene functional annotation
metasource: Fairsharing.org
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genome
metasource: Fairsharing.org
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molecular interaction
metasource: Fairsharing.org
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network model
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orthologous
metasource: Fairsharing.org
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protein
metasource: Fairsharing.org
version: None

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

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

genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:17.388699

genotype and phenotype
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:17.388699

gene expression gene functional annotation genome molecular interaction network model orthology protein plant genomics genotype and phenotype

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The Arabidopsis Information Resource

AraPheno

Arabidopsis MPSS

The Arabidopsis Gene Regulatory Information Server

AtPID

CATMA - Complete Arabidopsis Transcriptome MicroArray

Arabidopsis Mitochondrial Protein Database

ThaleMine

PLprot

NASCarrays (obsolete)

MAtDB2

ASRP - Arabidopsis Small RNA Project

SeedGenes

Arabidopsis Nucleolar Protein Database

RARGE - RIKEN Arabidopsis Genome Encyclopedia

Nottingham Arabidopsis Stock Centre Seeds Database

AthaMap

GEM2Net

Database of Arabidopsis Transcription Factors

Plant Metabolomics