ThaleMine
ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.
Description
More detailed information about this field from each metasource.
ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.
metasource: Fairsharing.orgversion: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
Webpage:
https://bar.utoronto.ca/thalemineWebpage
More detailed information about this field from each metasource.
https://bar.utoronto.ca/thalemine
metasource: Fairsharing.orgversion: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
Licence:
Name: LGPL-2.1Licence name
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
Araport: the Arabidopsis information portal
PMID: 25414324
metasource: Fairsharing.org
version: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://dx.doi.org/10.1093/bioinformatics/bts577
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
Publications
More detailed information about this field from each metasource.
Araport: the Arabidopsis information portal
PMID: 25414324
metasource: Fairsharing.org
version: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
http://dx.doi.org/10.1093/bioinformatics/bts577
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
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Araport: the Arabidopsis information portal
PubMed citations: 87.
87 articles citing: Araport: the Arabidopsis information portal
Effective Mechanisms for Improving Seed Oil Production in Pennycress (Thlaspi arvense L.) Highlighted by Integration of Comparative Metabolomics and Transcriptomics. PMID:35909773
APOK3, a pollen killer antidote in Arabidopsis thaliana. PMID:35666201
Recent Progress on Systems and Synthetic Biology of Diatoms for Improving Algal Productivity. PMID:35646842
ABI5 binding protein2 inhibits ABA responses during germination without ABA-INSENSITIVE5 degradation. PMID:35258597
Gene coexpression analysis in Arabidopsis thaliana based on public microarray data. PMID:35243384
Loss of a pyridoxal-phosphate phosphatase rescues Arabidopsis lacking an endoplasmic reticulum ATP carrier. PMID:35139220
Plant Reactome and PubChem: The Plant Pathway and (Bio)Chemical Entity Knowledgebases. PMID:35037224
Data Management and Modeling in Plant Biology. PMID:34539712
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
Transcriptomic Analysis of Radish (Raphanus sativus L.) Spontaneous Tumor. PMID:34063717
Isolation of Lipid Droplets for Protein and Lipid Analysis. PMID:34047983
Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids. PMID:33874976
PopAmaranth: A population genetic genome browser for grain amaranths and their wild relatives. PMID:33822034
Anno genominis XX: 20 years of Arabidopsis genomics. PMID:33793861
Mapping rRNA 2'-O-methylations and identification of C/D snoRNAs in Arabidopsis thaliana plants. PMID:33596769
Phototropin 1 and 2 Influence Photosynthesis, UV-C Induced Photooxidative Stress Responses, and Cell Death. PMID:33498294
Ustilago maydis effector Jsi1 interacts with Topless corepressor, hijacking plant jasmonate/ethylene signaling. PMID:33247447
Complexity of Brassica oleracea-Alternaria brassicicola Susceptible Interaction Reveals Downregulation of Photosynthesis at Ultrastructural, Transcriptional, and Physiological Levels. PMID:33092216
Identification and Analysis of microRNAs in Chlorella sorokiniana Using High-Throughput Sequencing. PMID:32992970
Molecular Characterization, Expression Pattern and Function Analysis of Glycine-Rich Protein Genes Under Stresses in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). PMID:32849790
Novel Role of JAC1 in Influencing Photosynthesis, Stomatal Conductance, and Photooxidative Stress Signalling Pathway in Arabidopsis thaliana. PMID:32849690
Developmentally controlled changes during Arabidopsis leaf development indicate causes for loss of stress tolerance with age. PMID:32720687
Network-guided search for genetic heterogeneity between gene pairs. PMID:32573681
High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PMID:32236090
Arabidopsis DNA Replication Initiates in Intergenic, AT-Rich Open Chromatin. PMID:32205451
Integrated multi-omics framework of the plant response to jasmonic acid. PMID:32170290
The persimmon genome reveals clues to the evolution of a lineage-specific sex determination system in plants. PMID:32069274
Plasticity of Phymatotrichopsis omnivora infection strategies is dependent on host and nonhost plant responses. PMID:31930733
Investigations into a putative role for the novel BRASSIKIN pseudokinases in compatible pollen-stigma interactions in Arabidopsis thaliana. PMID:31829135
Genetic and physiological mechanisms of freezing tolerance in locally adapted populations of a winter annual. PMID:31762012
The effector GpRbp-1 of Globodera pallida targets a nuclear HECT E3 ubiquitin ligase to modulate gene expression in the host. PMID:31756029
Plant Reactome: a knowledgebase and resource for comparative pathway analysis. PMID:31680153
Natural Variation Reveals a Key Role for Rhamnogalacturonan I in Seed Outer Mucilage and Underlying Genes. PMID:31591153
Degradation of the transcription factors PIF4 and PIF5 under UV-B promotes UVR8-mediated inhibition of hypocotyl growth in Arabidopsis. PMID:31571300
Identification of the Arabidopsis Calmodulin-Dependent NAD+ Kinase That Sustains the Elicitor-Induced Oxidative Burst. PMID:31554701
The specific molecular architecture of plant 3-hydroxy-3-methylglutaryl-CoA lyase. PMID:31515272
Evolutionary characteristics of intergenic transcribed regions indicate rare novel genes and widespread noisy transcription in the Poaceae. PMID:31431676
Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants. PMID:31316532
Root-specific camalexin biosynthesis controls the plant growth-promoting effects of multiple bacterial strains. PMID:31311863
SRAssembler: Selective Recursive local Assembly of homologous genomic regions. PMID:31266441
GeneNoteBook, a collaborative notebook for comparative genomics. PMID:31199463
Comparing time series transcriptome data between plants using a network module finding algorithm. PMID:31164912
The m6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants. PMID:31142640
Plant-necrotroph co-transcriptome networks illuminate a metabolic battlefield. PMID:31081752
Identification of a role for an E6-like 1 gene in early pollen-stigma interactions in Arabidopsis thaliana. PMID:31069543
A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. PMID:30886426
How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana. PMID:30726870
SOG1 activator and MYB3R repressors regulate a complex DNA damage network in Arabidopsis. PMID:30541889
Dissecting the functional domains of the Arabidopsis thaliana nonhost resistance 2B (AtNHR2B) protein. PMID:30325257
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. PMID:30239679
Hydrogen Peroxide: Its Role in Plant Biology and Crosstalk with Signalling Networks. PMID:30231521
Cytokinin at the Crossroads of Abiotic Stress Signalling Pathways. PMID:30126242
Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions. PMID:30111865
Arabidopsis thaliana ambient temperature responsive lncRNAs. PMID:30005624
Brachypodium: A Monocot Grass Model Genus for Plant Biology. PMID:29997238
Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs. PMID:29922309
Enhanced JBrowse plugins for epigenomics data visualization. PMID:29699480
Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story. PMID:29568308
A Vitis vinifera basic helix-loop-helix transcription factor enhances plant cell size, vegetative biomass and reproductive yield. PMID:29520945
MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. PMID:29220435
Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence. PMID:29202864
Salt Stress and CTD PHOSPHATASE-LIKE4 Mediate the Switch between Production of Small Nuclear RNAs and mRNAs. PMID:29093215
ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. PMID:28808136
N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana. PMID:28432195
Genomic and Phenomic Screens for Flower Related RING Type Ubiquitin E3 Ligases in Arabidopsis. PMID:28400782
ARA-PEPs: a repository of putative sORF-encoded peptides in Arabidopsis thaliana. PMID:28095775
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
Developing integrated crop knowledge networks to advance candidate gene discovery. PMID:28018846
Enhancing the GABI-Kat Arabidopsis thaliana T-DNA Insertion Mutant Database by Incorporating Araport11 Annotation. PMID:28013277
Lotus Base: An integrated information portal for the model legume Lotus japonicus. PMID:28008948
Ty1-copia elements reveal diverse insertion sites linked to polymorphisms among flax (Linum usitatissimum L.) accessions. PMID:27927184
Bio-TDS: bioscience query tool discovery system. PMID:27924016
AtPID: a genome-scale resource for genotype-phenotype associations in Arabidopsis. PMID:27899679
Plant Reactome: a resource for plant pathways and comparative analysis. PMID:27799469
Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. PMID:27791167
A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny. PMID:27711162
Raffinose Family Oligosaccharides Act As Galactose Stores in Seeds and Are Required for Rapid Germination of Arabidopsis in the Dark. PMID:27507985
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base. PMID:27433158
Extensive Natural Variation in Arabidopsis Seed Mucilage Structure. PMID:27375657
Integrating Large-Scale Data and RNA Technology to Protect Crops from Fungal Pathogens. PMID:27303409
JBrowse: a dynamic web platform for genome visualization and analysis. PMID:27072794
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. PMID:26989150
A cis-regulatory sequence from a short intergenic region gives rise to a strong microbe-associated molecular pattern-responsive synthetic promoter. PMID:26833485
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
Information Commons for Rice (IC4R). PMID:26519466
FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. PMID:26476447
The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. PMID:26201819 - http://dx.doi.org/10.1093/bioinformatics/bts577
Tags:
Tags
More detailed information about this field from each metasource.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
homologous
metasource: Fairsharing.org
version: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
data management
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
proteomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:57.432616
Tags
More detailed information about this field from each metasource.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
homologous
metasource: Fairsharing.orgversion: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
molecular interaction
metasource: Fairsharing.orgversion: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: ThaleMine; ThaleMine; DOI: https://doi.org/10.25504/FAIRsharing.0oOPKg; Last edited: Nov. 13, 2019, 6:58 a.m.; Last accessed: Jan 03 2022 7:05 p.m.
data management
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
proteomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:57.432616
gene gene expression homologous molecular interaction protein data management genomics proteomics
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