Tomato Functional Genomics Database

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More detailed information about this field from each metasource. ×

Tomato Functional Genomics Database

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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TED

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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TED - Tomato Functional Genomics Database

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

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Tomato Functional Genomics Database (TFGD)

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977

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tfgd

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977

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Other names: TED, TED - Tomato Functional Genomics Database, Tomato Functional Genomics Database (TFGD), tfgd

The Tomato Functional Genomics Database integrates several prior databases including the Tomato Expression Database and Tomato Metabolite Database, and the Tomato Small RNA Database.

Webpage:

Publications:

Publications

More detailed information about this field from each metasource. ×

Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics
PMID: 20965973

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977

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Tomato Expression Database (TED): a suite of data presentation and analysis tools
PMID: 16381976

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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http://nar.oxfordjournals.org/content/39/suppl_1/D1156

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

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• Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics PubMed citations: 52.

  52 articles citing: Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics

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  The tomato yellow leaf curl virus C4 protein alters the expression of plant developmental genes correlating to leaf upward cupping phenotype in tomato. PMID:35551312

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  Genome-Wide Analysis of the Protein Phosphatase 2C Genes in Tomato. PMID:35456410

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  An Integrated Bioinformatics and Functional Approach for miRNA Validation. PMID:35325428

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  Unprecedented organelle genomic variations in morning glories reveal independent evolutionary scenarios of parasitic plants and the diversification of plant mitochondrial complexes. PMID:35172831

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  Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato. PMID:34621298

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  New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis. PMID:34054921

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  Identification, Classification, and Expression Analysis of the Triacylglycerol Lipase (TGL) Gene Family Related to Abiotic Stresses in Tomato. PMID:33573234

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  Molecular characterization of SlATG18f in response to Tomato leaf curl New Delhi virus infection in tomato and development of a CAPS marker for leaf curl disease tolerance. PMID:33554270

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  Metabolic engineering of tomato fruit enriched in L-DOPA. PMID:33242649

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  Potato Virus Y Infection Alters Small RNA Metabolism and Immune Response in Tomato. PMID:31783643

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  Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato. PMID:31775241

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  Overexpression of MiR482c in Tomato Induces Enhanced Susceptibility to Late Blight. PMID:31382588

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  Comprehensive transcriptome analysis and functional characterization of PR-5 for its involvement in tomato Sw-7 resistance to tomato spotted wilt tospovirus. PMID:31114006

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  Identification and characterisation of microRNAs and their target genes in phosphate-starved Nicotiana benthamiana by small RNA deep sequencing and 5'RACE analysis. PMID:30558535

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  Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. PMID:30353370

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  Genome-wide comparative analysis in Solanaceous species reveals evolution of microRNAs targeting defense genes in Capsicum spp. PMID:30060137

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  Exploring the sound-modulated delay in tomato ripening through expression analysis of coding and non-coding RNAs. PMID:30010774

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  A comprehensive review of web-based resources of non-coding RNAs for plant science research. PMID:29989090

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  Genome-Wide Identification and Expression Analysis of the UGlcAE Gene Family in Tomato. PMID:29861481

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  A Systems Biology Study in Tomato Fruit Reveals Correlations between the Ascorbate Pool and Genes Involved in Ribosome Biogenesis, Translation, and the Heat-Shock Response. PMID:29491875

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  Genome-Wide Identification and Evaluation of Reference Genes for Quantitative RT-PCR Analysis during Tomato Fruit Development. PMID:28900431

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  Genome-wide analysis and expression profiling of zinc finger homeodomain (ZHD) family genes reveal likely roles in organ development and stress responses in tomato. PMID:28874115

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  Comprehensive transcriptome analyses reveal tomato plant responses to tobacco rattle virus-based gene silencing vectors. PMID:28852064

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  Co-expressed Pathways DataBase for Tomato: a database to predict pathways relevant to a query gene. PMID:28583129

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  SesameFG: an integrated database for the functional genomics of sesame. PMID:28539606

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  Comprehensive Transcriptome Analyses Reveal that Potato Spindle Tuber Viroid Triggers Genome-Wide Changes in Alternative Splicing, Inducible trans-Acting Activity of Phased Secondary Small Interfering RNAs, and Immune Responses. PMID:28331096

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  Identification of a Solanum pennellii Chromosome 4 Fruit Flavor and Nutritional Quality-Associated Metabolite QTL. PMID:27881988

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  The SOD Gene Family in Tomato: Identification, Phylogenetic Relationships, and Expression Patterns. PMID:27625661

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  Exploiting Genomics Resources to Identify Candidate Genes Underlying Antioxidants Content in Tomato Fruit. PMID:27092148

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  Identification and validation of a virus-inducible ta-siRNA-generating TAS4 locus in tomato. PMID:26949093

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  MIrExpress: A Database for Gene Coexpression Correlation in Immune Cells Based on Mutual Information and Pearson Correlation. PMID:26881263

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  A CURLY LEAF homologue controls both vegetative and reproductive development of tomato plants. PMID:26846417

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  Identification of key genes involved in root development of tomato using expressed sequence tag analysis. PMID:26600676

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  NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome. PMID:25849067

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  Comparative transcriptome analyses reveal core parasitism genes and suggest gene duplication and repurposing as sources of structural novelty. PMID:25534030

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  Functional genomics of tomato: opportunities and challenges in post-genome NGS era. PMID:25431420

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  Quantitative peptidomics study reveals that a wound-induced peptide from PR-1 regulates immune signaling in tomato. PMID:25361956

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  Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data. PMID:24832228

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  Tomato genomic resources database: an integrated repository of useful tomato genomic information for basic and applied research. PMID:24466070

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  Reduction of photosynthetic sensitivity in response to abiotic stress in tomato is mediated by a new generation plant activator. PMID:23898952

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  Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. PMID:23759993

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  System-wide hypersensitive response-associated transcriptome and metabolome reprogramming in tomato. PMID:23719893

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  Current challenges and future potential of tomato breeding using omics approaches. PMID:23641179

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  Galacturonosyltransferase 4 silencing alters pectin composition and carbon partitioning in tomato. PMID:23599271

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  Reuse of public genome-wide gene expression data. PMID:23269463

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  Differential modulation of photosynthesis, signaling, and transcriptional regulation between tolerant and sensitive tomato genotypes under cold stress. PMID:23226384

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  The tomato genome: implications for plant breeding, genomics and evolution. PMID:22943138

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  Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum. PMID:22570076

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  Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects. PMID:22350316

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  Exploring tomato gene functions based on coexpression modules using graph clustering and differential coexpression approaches. PMID:22307966

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  Advances in omics and bioinformatics tools for systems analyses of plant functions. PMID:22156726

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  Tissue- and cell-type specific transcriptome profiling of expanding tomato fruit provides insights into metabolic and regulatory specialization and cuticle formation. PMID:22045915
• Tomato Expression Database (TED): a suite of data presentation and analysis tools PubMed citations: 25.

  25 articles citing: Tomato Expression Database (TED): a suite of data presentation and analysis tools

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  Tomato Fruit Development and Metabolism. PMID:31850035

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  Advances in Omics Approaches for Abiotic Stress Tolerance in Tomato. PMID:31775241

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  PRGdb 3.0: a comprehensive platform for prediction and analysis of plant disease resistance genes. PMID:29156057

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  Ethylene Control of Fruit Ripening: Revisiting the Complex Network of Transcriptional Regulation. PMID:26511917

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  Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba. PMID:25577200

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  Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564

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  Spermidine affects the transcriptome responses to high temperature stress in ripening tomato fruit. PMID:22467370

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  Genome-wide investigation and expression analysis suggest diverse roles of auxin-responsive GH3 genes during development and response to different stimuli in tomato (Solanum lycopersicum). PMID:22228229

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  Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato. PMID:22212279

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  Genetic dissection of vitamin E biosynthesis in tomato. PMID:21527625

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  Genome-wide analysis of auxin response factor (ARF) gene family from tomato and analysis of their role in flower and fruit development. PMID:21290147

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  Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. PMID:20973957

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  Tomato Functional Genomics Database: a comprehensive resource and analysis package for tomato functional genomics. PMID:20965973

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  Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato. PMID:20643807

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  Combining genetic diversity, informatics and metabolomics to facilitate annotation of plant gene function. PMID:20539294

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  Stone formation in peach fruit exhibits spatial coordination of the lignin and flavonoid pathways and similarity to Arabidopsis dehiscence. PMID:20144217

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  Plant MetGenMAP: an integrative analysis system for plant systems biology. PMID:19819981

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  Comprehensive resources for tomato functional genomics based on the miniature model tomato micro-tom. PMID:19506732

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  Using metabolomics to estimate unintended effects in transgenic crop plants: problems, promises, and opportunities. PMID:19137102

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  SoyXpress: a database for exploring the soybean transcriptome. PMID:18671881

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  Heterologous microarray experiments allow the identification of the early events associated with potato tuber cold sweetening. PMID:18416834

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  ISOL@: an Italian SOLAnaceae genomics resource. PMID:18387209

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  MELOGEN: an EST database for melon functional genomics. PMID:17767721

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  TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species. PMID:17142232

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  Expression profiling of the 14-3-3 gene family in response to salt stress and potassium and iron deficiencies in young tomato (Solanum lycopersicum) roots: analysis by real-time RT-PCR. PMID:16943217
• http://nar.oxfordjournals.org/content/39/suppl_1/D1156

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More detailed information about this field from each metasource. ×

annotation

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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gene expression data

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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genome

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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metabolite

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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micro rna

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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rna sequence

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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ribonucleic acid

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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small interfering rna

metasource: Fairsharing.org
version: FAIRsharing.org: TED; Tomato Functional Genomics Database; DOI: https://doi.org/10.25504/FAIRsharing.dn2c0s; Last edited: April 26, 2021, 9:31 a.m.; Last accessed: Jan 03 2022 7:07 p.m.

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plant databases

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

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other plants

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

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small molecules

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977

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functional, regulatory and non-coding rna

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977

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gene expression

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977

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gene transcripts

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977

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molecular interactions, pathways and networks

metasource: bio.tools
version: extracted_at: 2022-11-04T11:33:33.769977

Close

gene expression genome metabolite micro rna rna sequence rna small interfering rna plant other plants small molecule functional, regulatory and non-coding rna gene expression gene transcripts molecular interactions, pathways and networks