IT3F: A web-based tool for functional analysis of transcription factors in plants

Phytochemistry

Volumn 69, Issue 13, 2008, Pages 2417-2425

  Bailey, Paul C ^a   Dicks, Jo ^a   Wang, Trevor L ^a   Martin, Cathie ^a  

^a NORWICH RESEARCH PARK   (United Kingdom)

Author keywords

Arabidopsis thaliana; bHLH; Gene expression; myb; Oryza sativa; PHYLIP; Phylogenetics; Transcription factor; Website

Indexed keywords

ARABIDOPSIS PROTEIN; BOTRYTIS SUSCEPTIBLE1 PROTEIN, ARABIDOPSIS; TRANSCRIPTION FACTOR; VEGETABLE PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; BIOLOGY; CLASSIFICATION; COMPUTER PROGRAM; GENETICS; INTERNET; METHODOLOGY; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; SEQUENCE HOMOLOGY; SHORT SURVEY;

ALGORITHMS; AMINO ACID SEQUENCE; ARABIDOPSIS PROTEINS; COMPUTATIONAL BIOLOGY; INTERNET; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; TRANSCRIPTION FACTORS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; ORYZA SATIVA;

EID: 53849085110     PISSN: 00319422     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.phytochem.2008.08.003     Document Type: Short Survey

References (49)

1. Arabidopsis Genome Initiative, 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815.
2. Blanc G., Hokamp K., and Wolfe K.H. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Research 13 (2003) 137-144
3. Briggs G.C., Osmont K.S., Shindo C., Sibout R., and Hardtke C.S. Unequal genetic redundancies in Arabidopsis-a neglected phenomenon?. Trends in Plant Science 11 (2006) 492-498
4. Conte M.G., Gaillard S., Lanau N., Rouard M., and Perin C. GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Research 36 (2008) D991-D998
5. Davuluri R.V., Sun H., Palaniswamy S.K., Matthews N., Molina C., Kurtz M., and Grotewold E. AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics 4 (2003) 25
6. Eddy, S.R., 1998. Profile hidden Markov models. Bioinformatics (Oxford, England) 14, 755-763.
7. Felsenstein J. PHYLIP (Phylogeny Inference Package) Version 3.6 Distributed by the Author (2004), Department of Genome Sciences, University of Washington, Seattle
8. Fredslund J. DATFAP: a database of primers and homology alignments for transcription factors from 13 plant species. BMC Genomics 9 (2008) 140
9. Frickey T., Benedito V.A., Udvardi M., and Weiller G. AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips. Plant Physiology 146 (2008) 377-386
10. Gao, G., Zhong, Y., Guo, A., Zhu, Q., Tang, W., Zheng, W., Gu, X., Wei, L., Luo, J., 2006. DRTF: a database of rice transcription factors. Bioinformatics (Oxford, England) 22, 1286-1287.
11. Grotewold E., Drummond B.J., Bowen B., and Peterson T. The myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset. Cell 76 (1994) 543-553
12. Guo, A., He, K., Liu, D., Bai, S., Gu, X., Wei, L., Luo, J., 2005. DATF: a database of Arabidopsis transcription factors. Bioinformatics (Oxford, England) 21, 2568-2569.
13. 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. PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Research 36 (2008) D966-D969
14. Heim M.A., Jakoby M., Werber M., Martin C., Weisshaar B., and Bailey P.C. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Molecular Biology and Evolution 20 (2003) 735-747
15. Iida K., Seki M., Sakurai T., Satou M., Akiyama K., Toyoda T., Konagaya A., and Shinozaki K. RARTF: database and tools for complete sets of Arabidopsis transcription factors. DNA Research 12 (2005) 247-256
16. Jaillon O., Aury J.M., Noel B., Policriti A., Clepet C., Casagrande A., Choisne N., Aubourg S., Vitulo N., Jubin C., Vezzi A., Legeai F., Hugueney P., Dasilva C., Horner D., Mica E., Jublot D., Poulain J., Bruyere C., Billault A., Segurens B., Gouyvenoux M., Ugarte E., Cattonaro F., Anthouard V., Vico V., Del Fabbro C., Alaux M., Di Gaspero G., Dumas V., Felice N., Paillard S., Juman I., Moroldo M., Scalabrin S., Canaguier A., Le Clainche I., Malacrida G., Durand E., Pesole G., Laucou V., Chatelet P., Merdinoglu D., Delledonne M., Pezzotti M., Lecharny A., Scarpelli C., Artiguenave F., Pe M.E., Valle G., Morgante M., Caboche M., Adam-Blondon A.F., Weissenbach J., Quetier F., and Wincker P. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449 (2007) 463-467
17. Jain M., Nijhawan A., Arora R., Agarwal P., Ray S., Sharma P., Kapoor S., Tyagi A.K., and Khurana J.P. F-box proteins in rice. Genome-wide analysis, classification, temporal and spatial gene expression during panicle and seed development, and regulation by light and abiotic stress. Plant Physiology 143 (2007) 1467-1483
18. Jin H., Cominelli E., Bailey P., Parr A., Mehrtens F., Jones J., Tonelli C., Weisshaar B., and Martin C. Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis. The EMBO Journal 19 (2000) 6150-6161
19. Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8 (1992) 275-282
20. Kilian J., Whitehead D., Horak J., Wanke D., Weinl S., Batistic O., D'Angelo C., Bornberg-Bauer E., Kudla J., and Harter K. The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant Journal 50 (2007) 347-363
21. Kuhner M.K., and Felsenstein J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Molecular Biology and Evolution 11 (1994) 459-468
22. Lee, M.M., Schiefelbein, J., 2001. Developmentally distinct MYB genes encode functionally equivalent proteins in Arabidopsis. Development (Cambridge, England) 128, 1539-1546.
23. Li X., Duan X., Jiang H., Sun Y., Tang Y., Yuan Z., Guo J., Liang W., Chen L., Yin J., Ma H., Wang J., and Zhang D. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiology 141 (2006) 1167-1184
24. Liu L., White M.J., and MacRae T.H. Transcription factors and their genes in higher plants functional domains, evolution and regulation. European Journal of Biochemistry/FEBS 262 (1999) 247-257
25. Luo J., Nishiyama Y., Fuell C., Taguchi G., Elliott K., Hill L., Tanaka Y., Kitayama M., Yamazaki M., Bailey P., Parr A., Michael A.J., Saito K., and Martin C. Convergent evolution in the BAHD family of acyl transferases: identification and characterization of anthocyanin acyl transferases from Arabidopsis thaliana. Plant Journal 50 (2007) 678-695
26. Manfield I.W., Jen C.H., Pinney J.W., Michalopoulos I., Bradford J.R., Gilmartin P.M., and Westhead D.R. Arabidopsis Co-expression Tool (ACT): web server tools for microarray-based gene expression analysis. Nucleic Acids Research 34 (2006) W504-W509
27. Martin C., and Paz-Ares J. MYB transcription factors in plants. Trends Genetics 13 (1997) 67-73
28. Ming R., Hou S., Feng Y., Yu Q., Dionne-Laporte A., Saw J.H., Senin P., Wang W., Ly B.V., Lewis K.L., Salzberg S.L., Feng L., Jones M.R., Skelton R.L., Murray J.E., Chen C., Qian W., Shen J., Du P., Eustice M., Tong E., Tang H., Lyons E., Paull R.E., Michael T.P., Wall K., Rice D.W., Albert H., Wang M.L., Zhu Y.J., Schatz M., Nagarajan N., Acob R.A., Guan P., Blas A., Wai C.M., Ackerman C.M., Ren Y., Liu C., Wang J., Wang J., Na J.K., Shakirov E.V., Haas B., Thimmapuram J., Nelson D., Wang X., Bowers J.E., Gschwend A.R., Delcher A.L., Singh R., Suzuki J.Y., Tripathi S., Neupane K., Wei H., Irikura B., Paidi M., Jiang N., Zhang W., Presting G., Windsor A., Navajas-Perez R., Torres M.J., Feltus F.A., Porter B., Li Y., Burroughs A.M., Luo M.C., Liu L., Christopher D.A., Mount S.M., Moore P.H., Sugimura T., Jiang J., Schuler M.A., Friedman V., Mitchell-Olds T., Shippen D.E., dePamphilis C.W., Palmer J.D., Freeling M., Paterson A.H., Gonsalves D., Wang L., and Alam M. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452 (2008) 991-996
29. Nakano T., Suzuki K., Fujimura T., and Shinshi H. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiology 140 (2006) 411-432
30. Niggeweg R., Michael A.J., and Martin C. Engineering plants with increased levels of the antioxidant chlorogenic acid. Nature Biotechnology 22 (2004) 746-754
31. Olsen G.J., Matsuda H., Hagstrom R., and Overbeek R. FastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Computer Applications in the Biosciences 10 (1994) 41-48
32. Remm M., Storm C.E., and Sonnhammer E.L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. Journal of Molecular Biology 314 (2001) 1041-1052
33. Rensing, S.A., Lang, D., Zimmer, A.D., Terry, A., Salamov, A., Shapiro, H., Nishiyama, T., Perroud, P.F., Lindquist, E.A., Kamisugi, Y., Tanahashi, T., Sakakibara, K., Fujita, T., Oishi, K., Shin, I.T., Kuroki, Y., Toyoda, A., Suzuki, Y., Hashimoto, S., Yamaguchi, K., Sugano, S., Kohara, Y., Fujiyama, A., Anterola, A., Aoki, S., Ashton, N., Barbazuk, W.B., Barker, E., Bennetzen, J.L., Blankenship, R., Cho, S.H., Dutcher, S.K., Estelle, M., Fawcett, J.A., Gundlach, H., Hanada, K., Heyl, A., Hicks, K.A., Hughes, J., Lohr, M., Mayer, K., Melkozernov, A., Murata, T., Nelson, D.R., Pils, B., Prigge, M., Reiss, B., Renner, T., Rombauts, S., Rushton, P.J., Sanderfoot, A., Schween, G., Shiu, S.H., Stueber, K., Theodoulou, F.L., Tu, H., Van de Peer, Y., Verrier, P.J., Waters, E., Wood, A., Yang, L., Cove, D., Cuming, A.C., Hasebe, M., Lucas, S., Mishler, B.D., Reski, R., Grigoriev, I.V., Quatrano, R.S., Boore, J.L., 2008. The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (New York, NY) 319, 64-69.
34. Riano-Pachon D.M., Ruzicic S., Dreyer I., and Mueller-Roeber B. PlnTFDB: an integrative plant transcription factor database. BMC Bioinformatics 8 (2007) 42
35. Richardt S., Lang D., Reski R., Frank W., and Rensing S.A. PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins. Plant Physiology 143 (2007) 1452-1466
36. Riechmann, J.L., Heard, J., Martin, G., Reuber, L., Jiang, C., Keddie, J., Adam, L., Pineda, O., Ratcliffe, O.J., Samaha, R.R., Creelman, R., Pilgrim, M., Broun, P., Zhang, J.Z., Ghandehari, D., Sherman, B.K., Yu, G., 2000. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science (New York, NY) 290, 2105-2110.
37. Riechmann J.L., and Meyerowitz E.M. The AP2/EREBP family of plant transcription factors. Biological Chemistry 379 (1998) 633-646
38. Saitou N., and Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4 (1987) 406-425
39. Schmid M., Davison T.S., Henz S.R., Pape U.J., Demar M., Vingron M., Scholkopf B., Weigel D., and Lohmann J.U. A gene expression map of Arabidopsis thaliana development. Nature Genetics 37 (2005) 501-506
40. Shiu S.H., Shih M.C., and Li W.H. Transcription factor families have much higher expansion rates in plants than in animals. Plant Physiology 139 (2005) 18-26
41. Sieweke M.H., and Graf T. A transcription factor party during blood cell differentiation. Current Opinion in Genetics & Development 8 (1998) 545-551
42. Soltis D.E., Albert V.A., Leebens-Mack J., Palmer J.D., Wing R.A., dePamphilis C.W., Ma H., Carlson J.E., Altman N., Kim S., Wall P.K., Zuccolo A., and Soltis P.S. The Amborella genome: an evolutionary reference for plant biology. Genome Biology 9 (2008) 402
43. Spencer M.W., Casson S.A., and Lindsey K. Transcriptional profiling of the Arabidopsis embryo. Plant Physiology 143 (2007) 924-940
44. Stracke R., Werber M., and Weisshaar B. The R2R3-MYB gene family in Arabidopsis thaliana. Current Opinion in Plant Biology 4 (2001) 447-456
45. Tamagnone L., Merida A., Parr A., Mackay S., Culianez-Macia F.A., Roberts K., and Martin C. The AmMYB308 and AmMYB330 transcription factors from antirrhinum regulate phenylpropanoid and lignin biosynthesis in transgenic tobacco. Plant Cell 10 (1998) 135-154
46. Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., Schein, J., Sterck, L., Aerts, A., Bhalerao, R.R., Bhalerao, R.P., Blaudez, D., Boerjan, W., Brun, A., Brunner, A., Busov, V., Campbell, M., Carlson, J., Chalot, M., Chapman, J., Chen, G.L., Cooper, D., Coutinho, P.M., Couturier, J., Covert, S., Cronk, Q., Cunningham, R., Davis, J., Degroeve, S., Dejardin, A., Depamphilis, C., Detter, J., Dirks, B., Dubchak, I., Duplessis, S., Ehlting, J., Ellis, B., Gendler, K., Goodstein, D., Gribskov, M., Grimwood, J., Groover, A., Gunter, L., Hamberger, B., Heinze, B., Helariutta, Y., Henrissat, B., Holligan, D., Holt, R., Huang, W., Islam-Faridi, N., Jones, S., Jones-Rhoades, M., Jorgensen, R., Joshi, C., Kangasjarvi, J., Karlsson, J., Kelleher, C., Kirkpatrick, R., Kirst, M., Kohler, A., Kalluri, U., Larimer, F., Leebens-Mack, J., Leple, J.C., Locascio, P., Lou, Y., Lucas, S., Martin, F., Montanini, B., Napoli, C., Nelson, D.R., Nelson, C., Nieminen, K., Nilsson, O., Pereda, V., Peter, G., Philippe, R., Pilate, G., Poliakov, A., Razumovskaya, J., Richardson, P., Rinaldi, C., Ritland, K., Rouze, P., Ryaboy, D., Schmutz, J., Schrader, J., Segerman, B., Shin, H., Siddiqui, A., Sterky, F., Terry, A., Tsai, C.J., Uberbacher, E., Unneberg, P., Vahala, J., Wall, K., Wessler, S., Yang, G., Yin, T., Douglas, C., Marra, M., Sandberg, G., Van de Peer, Y., Rokhsar, D., 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science (New York, NY) 313, 1596-1604.
47. Yanhui C., Xiaoyuan Y., Kun H., Meihua L., Jigang L., Zhaofeng G., Zhiqiang L., Yunfei Z., Xiaoxiao W., Xiaoming Q., Yunping S., Li Z., Xiaohui D., Jingchu L., Xing-Wang D., Zhangliang C., Hongya G., and Li-Jia Q. The MYB transcription factor superfamily of Arabidopsis: expression analysis and phylogenetic comparison with the rice MYB family. Plant Molecular Biology 60 (2006) 107-124
48. Zimmermann I.M., Heim M.A., Weisshaar B., and Uhrig J.F. Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins. Plant Journal 40 (2004) 22-34
49. Zmasek C.M., and Eddy S.R. RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 3 (2002) 14