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TFGD specifications


Unique identifier OMICS_27255
Alternative name Tomato Functional Genomics Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes


  • person_outline Zhangjun Fei
  • person_outline James Giovannoni

Publications for Tomato Functional Genomics Database

TFGD citations


Genome Wide Identification and Evaluation of Reference Genes for Quantitative RT PCR Analysis during Tomato Fruit Development

Front Plant Sci
PMCID: 5581943
PMID: 28900431
DOI: 10.3389/fpls.2017.01440
call_split See protocol

[…] able . The corresponding gene sequences of these candidate RGs were collected from NCBI (National Center for Biotechnology Information:, SGN (, TFGD ( (Fraser et al., ), and CuGenDB ( Through Blastn search, the orthologous genes (E-value was set at 1e−5) were collected in tomato genome databa […]


Identification of Optimal Reference Genes for Normalization of qPCR Analysis during Pepper Fruit Development

Front Plant Sci
PMCID: 5489665
PMID: 28706523
DOI: 10.3389/fpls.2017.01128
call_split See protocol

[…] iption, are listed in Table . The corresponding gene sequences of these candidate RGs were then collected from the NCBI (National Center for Biotechnology Information:; TFGD (Tomato Functional Genomics Database:; and CuGenDB (Cucurbit Genomics Database:, respectively. Then, using a Blastn search, the orthologous gen […]


Compositionally distinct nuclear pore complexes of functionally distinct dimorphic nuclei in the ciliate Tetrahymena

PMCID: 5450191
PMID: 28386019
DOI: 10.1242/jcs.199398
call_split See protocol

[…] for candidates Nups using protein BLAST on the NCBI website and Tetrahymena Genome Database Wiki ( (; ). Expression profiles based on microarray data ( were obtained from the TetraFGD ( (). We identified the candidate proteins as Nups when the expression profile satisfied two conditions: first, that the […]


Nonsense mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa specific nuclease

Nucleic Acids Res
PMCID: 5499736
PMID: 28402567
DOI: 10.1093/nar/gkx256
call_split See protocol

[…] sing ESPript 3.0 (). Phylogenetic trees were constructed using Mega5 with default settings (neighbor-joining method) (). Gene expression profiles shown in Figure were retrieved from TetraFGD ( (). […]


A Zip3 like protein plays a role in crossover formation in the SC less meiosis of the protist Tetrahymena

Mol Biol Cell
PMCID: 5349789
PMID: 28100637
DOI: 10.1091/mbc.E16-09-0678

[…] HERM_00049220, previously known as COI20 (for Conjugation Induced; ), because it is specifically expressed in cells at the early conjugation stage, that is, when meiosis takes place (TetraFGD;; ; ). The predicted protein, TTHERM 00049220p, consists of 415 amino acids and has a molecular weight of 49.6 kDa. Orthologous proteins can be identified in Tetrahymena ellioti, Tetrahy […]


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

Front Plant Sci
PMCID: 5003820
PMID: 27625661
DOI: 10.3389/fpls.2016.01279

[…] For RNA-seq analysis, transcription data of the genome-wide gene expression of the tomato cultivar Helnz were downloaded from the tomato functional genomics database (TFGD) (). Ten different tissues were selected: root, leaf, bud, flower, 1-cm fruit, 2-cm fruit, 3-cm fruit, mature green fruit (MG), fruit at the fruit breaking st […]


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TFGD institution(s)
Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY, USA; USDA Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA; Plant Molecular and Cellular Biology Program, Horticultural Sciences, University of Florida, Gainesville, FL, USA
TFGD funding source(s)
Supported by National Science Foundation (IOS-0501778 and IOS-0923312).

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