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Protocols

TFGD specifications

Information


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

Maintainers


  • person_outline Zhangjun Fei
  • person_outline James Giovannoni

Publications for Tomato Functional Genomics Database

TFGD citations

 (21)
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Genome Wide Identification and Evaluation of Reference Genes for Quantitative RT PCR Analysis during Tomato Fruit Development

2017
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: https://www.ncbi.nlm.nih.gov/), SGN (https://solgenomics.net/), TFGD (http://ted.bti.cornell.edu/) (Fraser et al., ), and CuGenDB (http://www.icugi.org/). Through Blastn search, the orthologous genes (E-value was set at 1e−5) were collected in tomato genome databa […]

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

2017
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: https://www.ncbi.nlm.nih.gov/); TFGD (Tomato Functional Genomics Database: http://ted.bti.cornell.edu/); and CuGenDB (Cucurbit Genomics Database: http://www.icugi.org/), respectively. Then, using a Blastn search, the orthologous gen […]

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

2017
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 (http://ciliate.org/index.php/home/welcome) (; ). Expression profiles based on microarray data (http://tfgd.ihb.ac.cn/tool/exp) were obtained from the TetraFGD (http://tfgd.ihb.ac.cn/) (). We identified the candidate proteins as Nups when the expression profile satisfied two conditions: first, that the […]

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

2017
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 (http://tfgd.ihb.ac.cn/) (). […]

library_books

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

2017
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; http://tfgd.ihb.ac.cn; ; ). 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 […]

library_books

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

2016
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 […]

Citations

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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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