PlantTFDB 3.0: A portal for the functional and evolutionary study of plant transcription factors

Nucleic Acids Research

Volumn 42, Issue D1, 2014, Pages

  Jin, Jinpu ^a   Zhang, He ^a,b   Kong, Lei ^a   Gao, Ge ^a   Luo, Jingchu ^a  

^a PEKING UNIVERSITY   (China)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLANT TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; VEGETABLE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; EVOLUTIONARY DEVELOPMENTAL BIOLOGY; FUNCTIONAL ASSESSMENT; FUNCTIONAL PROTEOMICS; GENE SEQUENCE; NONHUMAN; PHENOTYPE; PHYLOGENETIC TREE; PLANTTFDB 3.0 DATABASE; PRIORITY JOURNAL; SPECIES IDENTIFICATION; VIRIDIPLANTAE; CLASSIFICATION; GENETICS; INTERNET; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; PLANT GENOME; PROTEIN DATABASE; ARABIDOPSIS THALIANA; CONTROLLED STUDY; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE IDENTIFICATION; GENE INTERACTION; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC REGULATION; GENETIC TRANSCRIPTION; INFORMATION PROCESSING; MOLECULAR EVOLUTION; ORTHOLOGY; PLANTTFDB; PREDICTION; PROTEOMICS; TAXONOMIC RANK;

DATABASES, PROTEIN; GENOME, PLANT; INTERNET; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; PLANT PROTEINS; TRANSCRIPTION FACTORS;

VIRIDIPLANTAE;

EID: 84891810676     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1016     Document Type: Article

References (39)

1. Riechmann, J., Heard, J., Martin, G., Reuber, L., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O., Samaha, R. and Creelman, R. (2000) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 290, 2105-2110.
2. Perez-Rodriguez, P., Riano-Pachon, D.M., Correa, L.G.G., Rensing, S.A., Kersten, B. and Mueller-Roeber, B. (2010) PlnTFDB: updated content and new features of the plant transcription factor database. Nucleic Acids Res., 38, D822-D827.
3. Richardt, S., Lang, D., Reski, R., Frank, W. and Rensing, S.A. (2007) PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiol., 143, 1452-1466.
4. Yilmaz, A., Nishiyama, M.Y. Jr, Fuentes, B.G., Souza, G.M., Janies, D., Gray, J. and Grotewold, E. (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiol., 149, 171-180.
5. Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.S. (2010) LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors. Bioinformatics, 26, 290-291.
6. Fredslund, J. (2008) DATFAP: a database of primers and homology alignments for transcription factors from 13 plant species. BMC Genomics, 9, 140.
7. Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K. and Tran, L.-S.P. (2013) TreeTFDB: An Integrative Database of the Transcription Factors from Six Economically Important Tree Crops for Functional Predictions and Comparative and Functional Genomics. DNA Res., 20, 151-162.
8. Yilmaz, A., Mejia-Guerra, M.K., Kurz, K., Liang, X., Welch, L. and Grotewold, E. (2011) AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. Nucleic Acids Res., 39, D1118-D1122.
9. Iida, K., Seki, M., Sakurai, T., Satou, M., Akiyama, K., Toyoda, T., Konagaya, A. and Shinozaki, K. (2005) RARTF: database and tools for complete sets of Arabidopsis transcription factors. DNA Res., 12, 247-256.
10. Rushton, P.J., Bokowiec, M.T., Laudeman, T.W., Brannock, J.F., Chen, X. and Timko, M.P. (2008) TOBFAC: the database of tobacco transcription factors. BMC Bioinformatics, 9, 53.
11. Wang, Z., Libault, M., Joshi, T., Valliyodan, B., Nguyen, H., Xu, D., Stacey, G. and Cheng, J. (2010) SoyDB: a knowledge database of soybean transcription factors. BMC Plant Biol., 10, 14.
12. Romeuf, I., Tessier, D., Dardevet, M., Branlard, G., Charmet, G. and Ravel, C. (2010) wDBTF: an integrated database resource for studying wheat transcription factor families. BMC Genomics, 11, 185.
13. Guo, A., He, K., Liu, D., Bai, S., Gu, X., Wei, L. and Luo, J. (2005) DATF: a database of Arabidopsis transcription factors. Bioinformatics, 21, 2568-2569.
14. Gao, G., Zhong, Y., Guo, A., Zhu, Q., Tang, W., Zheng, W., Gu, X., Wei, L. and Luo, J. (2006) DRTF: a database of rice transcription factors. Bioinformatics, 22, 1286-1287.
15. Zhu, Q.H., Guo, A.Y., Gao, G., Zhong, Y.F., Xu, M., Huang, M. and Luo, J. (2007) DPTF: a database of poplar transcription factors. Bioinformatics, 23, 1307-1308.
16. Guo, A.Y., Chen, X., Gao, G., Zhang, H., Zhu, Q.H., Liu, X.C., Zhong, Y.F., Gu, X., He, K. and Luo, J. (2008) PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Res., 36, D966-D969.
17. Zhang, H., Jin, J., Tang, L., Zhao, Y., Gu, X., Gao, G. and Luo, J. (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Res., 39, D1114-D1117.
18. Acland, A., Agarwala, R., Barrett, T., Beck, J., Benson, D.A., Bollin, C., Bolton, E., Bryant, S.H., Canese, K. and Church, D.M. (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 41, D8-D20.
19. Duvick, J., Fu, A., Muppirala, U., Sabharwal, M., Wilkerson, M.D., Lawrence, C.J., Lushbough, C. and Brendel, V. (2008) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res., 36, D959-D965.
20. Reinhold, H., Soyk, S., Simkova, K., Hostettler, C., Marafino, J., Mainiero, S., Vaughan, C.K., Monroe, J.D. and Zeeman, S.C. (2011) b-Amylase-Like Proteins Function as Transcription Factors in Arabidopsis, Controlling Shoot Growth and Development. Plant Cell, 23, 1391-1403.
21. Punta, M., Coggill, P.C., Eberhardt, R.Y., Mistry, J., Tate, J., Boursnell, C., Pang, N., Forslund, K., Ceric, G. and Clements, J. (2012) The Pfam protein families database. Nucleic Acids Res., 40, D290-D301.
22. Eddy, S. (2010) HMMER User's Guide: Biological sequence analysis using profile hidden Markov models (http://hmmer.org) (18 October 2013, date last accessed).
23. Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T.K., Bateman, A., Bernard, T., Binns, D., Bork, P., Burge, S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res., 40, D306-D312.
24. Cokol, M., Nair, R. and Rost, B. (2000) Finding nuclear localization signals. EMBO Rep., 1, 411-415.
25. Notredame, C., Higgins, D.G. and Heringa, J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
26. Price, M.N., Dehal, P.S. and Arkin, A.P. (2010) FastTree 2- approximately maximum-likelihood trees for large alignments. PLoS One, 5, e9490.
27. Ronquist, F. and Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
28. Van Bel, M., Proost, S., Wischnitzki, E., Movahedi, S., Scheerlinck, C., Van de Peer, Y. and Vandepoele, K. (2012) Dissecting plant genomes with the PLAZA comparative genomics platform. Plant Physiol., 158, 590-600.
29. Enright, A.J., Van Dongen, S. and Ouzounis, C.A. (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res., 30, 1575-1584.
30. Li, L., Stoeckert, C.J. and Roos, D.S. (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res., 13, 2178-2189.
31. Nystedt, B., Street, N.R., Wetterbom, A., Zuccolo, A., Lin, Y.-C., Scofield, D.G., Vezzi, F., Delhomme, N., Giacomello, S. and Alexeyenko, A. (2013) The Norway spruce genome sequence and conifer genome evolution. Nature, 497, 579-584.
32. Lang, D., Weiche, B., Timmerhaus, G., Richardt, S., Riano-Pachon, D.M., Correa, L.G., Reski, R., Mueller-Roeber, B. and Rensing, S.A. (2010) Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol. Evol., 2, 488-503.
33. Maglott, D., Ostell, J., Pruitt, K.D. and Tatusova, T. (2011) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res., 39, D52-D57.
34. Consortium, U. (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res., 41, D43-D47.
35. Baxter, L., Jironkin, A., Hickman, R., Moore, J., Barrington, C., Krusche, P., Dyer, N.P., Buchanan-Wollaston, V., Tiskin, A. and Beynon, J. (2012) Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. Plant Cell, 24, 3949-3965.
36. Haudry, A., Platts, A.E., Vello, E., Hoen, D.R., Leclercq, M., Williamson, R.J., Forczek, E., Joly-Lopez, Z., Steffen, J.G. and Hazzouri, K.M. (2013) An atlas of over 90, 000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat. Genet., 45, 891-898.
37. Hupalo, D. and Kern, A.D. (2013) Conservation and functional element discovery in 20 angiosperm plant genomes. Mol. Biol. Evol., 30, 1729-1744.
38. Shulaev, V., Sargent, D.J., Crowhurst, R.N., Mockler, T.C., Folkerts, O., Delcher, A.L., Jaiswal, P., Mockaitis, K., Liston, A., Mane, S.P. et al. (2011) The genome of woodland strawberry (Fragaria vesca). Nat. Genet., 43, 109-116.
39. Jia, J., Zhao, S., Kong, X., Li, Y., Zhao, G., He, W., Appels, R., Pfeifer, M., Tao, Y., Zhang, X. et al. (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature, 496, 91-95.