Comprehensive Transcription Factor Database for Plants

Currently, PlantTFDB contains TFs identified in 22 species (Table 1). Genome sequences of Arabidopsis (A. thaliana), rice (Oryza sativa), poplar (Populus trichocarpa), green alga (Chlamydomonas reinhardtii) and moss (Physcomitrella patens) were downloaded from TAIR, TIGR and JGI. For the 17 species without available complete genome data, we downloaded the unique transcripts from the Plant Genome Database (PlantGDB, http://www.plantgdb.org/) (10 (link)). These plant unique transcripts (PUTs) were assembled by PlantGDB based on the mRNA and EST sequences. We applied the framefinder program in ESTate (Expressed Sequence Tag Analysis Tools Etc) package to predict the open reading frames and obtain protein sequences from these PUTs (http://www.ebi.ac.uk/~guy/estate/).

Table 1.

Basic information of 22 species and TFs in the current PlantTFDB

Data source (Version)^a	Name		Species	TFs^b	TFs With Orthologs^c
TAIR (v6)	Arabidopsis		Arabidopsis thaliana	2290	1346
JGI (v1.1)	Poplar		Populus trichocarpa	2576	2042
TIGR (v4.0)	Rice		Oryza sativa (ssp. indica)	2025	1763
			Oryza sativa (ssp. japonica)	2384	2124
JGI (v1.1)	Moss		Physcomitrella patens	1170	524
JGI (v3.0)	Green alga		Chlamydomonas reinhardtii	205	64
PlantGDB (v155a)	Crops	Barley	Hordeum vulgare	618	595
	Maize		Zea mays	764	734
		Sorghum	Sorghum bicolor	397	372
		Sugarcane	Saccharum officinarum	1177	1157
		Wheat	Triticum aestivum	1127	1074
	Fruits	Apple	Malus domestica	1025	938
		Grape	Vitis vinifera	867	793
		Orange	Citrus sinensis	599	541
	Trees	Pine	Pinus taeda	950	644
		Spruce	Picea glauca	440	383
	Economic plants	Cotton	Gossypium hirsutum	1567	1430
		Potato	Solanum tuberosum	1340	1243
		Soybean	Glycine max	1891	1774
		Sunflower	Helianthus annuus	513	435
		Tomato	Lycopersicon esculentum	998	917
		Deervetch	Lotus japonicus	457	434
		Medicago	Medicago truncatula	1022	914

TAIR: The Arabidopsis Information Resource, http://www.arabidopsis.org/; TIGR: The Institute for Genomic Research, http://www.tigr.org/; JGI: DOE Joint Genome Institute, http://genome.jgi-psf.org/; PlantGDB: Plant Genome DataBase, http://www.plantgdb.org/.

The TF numbers of Arabidopsis and japonica rice are the number of gene models including alternative splicing.

The number of TFs of each species that has orthologs in all other species.

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Guo A.Y., Chen X., Gao G., Zhang H., Zhu Q.H., Liu X.C., Zhong Y.F., Gu X., He K, & Luo J. (2007). PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Research, 36(Database issue), D966-D969.

Publication 2007

A thaliana Arabidopsis Chlamydomonas reinhardtii Genome Joint Moss Mrna Open reading frames Oryza sativa Physcomitrella Plant Plant genome Plant protein Populus Protein sequences Rice Sequence analysis

Corresponding Organization : Peking University

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Variable analysis

independent variables

Genome sequences of Arabidopsis (A. thaliana), rice (Oryza sativa), poplar (Populus trichocarpa), green alga (Chlamydomonas reinhardtii) and moss (Physcomitrella patens) were downloaded from TAIR, TIGR and JGI.
For the 17 species without available complete genome data, unique transcripts were downloaded from the Plant Genome Database (PlantGDB).

dependent variables

Not explicitly mentioned.

control variables

Not explicitly mentioned.

controls

No positive or negative controls were specified.

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