ArchaeaTF: An integrated database of putative transcription factors in Archaea

Genomics

Volumn 91, Issue 1, 2008, Pages 102-107

  Wu, Jinyu ^a   Wang, Shengqin ^a   Bai, Jie ^a   Shi, Liang ^a   Li, Dong ^a   Xu, Zuyuan ^a   Niu, Yuxin ^a   Lu, Jianxin ^a   Bao, Qiyu ^a  

^a WENZHOU MEDICAL UNIVERSITY   (China)

Author keywords

Archaea; Comparative genomics; Database; Transcription factors

Indexed keywords

TRANSCRIPTION FACTOR;

ARCHAEBACTERIUM; ARTICLE; DATA BASE; DNA BINDING; GENOME; GENOMICS; NONHUMAN; ORTHOLOGY; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; TRANSCRIPTION REGULATION;

ARCHAEA; ARCHAEAL PROTEINS; DATABASES, PROTEIN; DNA-BINDING PROTEINS; INTERNET; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION FACTORS;

ARCHAEA; PROKARYOTA;

EID: 37349055176     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2007.09.007     Document Type: Article

References (32)

1. Blais A., and Dynlacht B.D. Constructing transcriptional regulatory networks. Genes Dev. 19 (2005) 1499-1511
2. Rodriguez-Caso C., Medina M.A., and Sole R.V. Topology, tinkering and evolution of the human transcription factor network. FEBS J. 272 (2005) 6423-6434
3. Kim T.H., and Ren B. Genome-wide analysis of protein-DNA interactions. Annu. Rev. Genomics Hum. Genet. 7 (2006) 81-102
4. Walhout A.J. Unraveling transcription regulatory networks by protein-DNA and protein-protein interaction mapping. Genome Res. 16 (2006) 1445-1454
5. Matys V., Kel-Margoulis O.V., Fricke E., Liebich I., Land S., Barre-Dirrie A., Reuter I., Chekmenev D., Krull M., Hornischer K., Voss N., Stegmaier P., Lewicki-Potapov B., Saxel H., Kel A.E., and Wingender E. Transfac and its module transcompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34 (2006) D108-D110
6. Makita Y., Nakao M., Ogasawara N., and Nakai K. DBTBS: Database of transcriptional regulation in bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res. 32 (2004) D75-D77
7. Martinez-Bueno M., Molina-Henares A.J., Pareja E., Ramos J.L., and Tobes R. Bactregulators: A database of transcriptional regulators in bacteria and archaea. Bioinformatics 20 (2004) 2787-2791
8. Tobes R., and Ramos J.L. Arac-XylS database: A family of positive transcriptional regulators in bacteria. Nucleic Acids Res. 30 (2002) 318-321
9. Wu J., Zhao F., Wang S., Deng G., Wang J., Bai J., Lu J., Qu J., and Bao Q. cTFbase: A database for comparative genomics of transcription factors in cyanobacteria. BMC Genomics 8 (2007) 104
10. Hermoso A., Aguilar D., Aviles F.X., and Querol E. TrSDB: A proteome database of transcription factors. Nucleic Acids Res. 32 (2004) D171-D173
11. Gao G., Zhong Y., Guo A., Zhu Q., Tang W., Zheng W., Gu X., Wei L., and Luo J. DRTF: A database of rice transcription factors. Bioinformatics 22 (2006) 1286-1287
12. Guo A., He K., Liu D., Bai S., Gu X., Wei L., and Luo J. DATF: A database of arabidopsis transcription factors. Bioinformatics 21 (2005) 2568-2569
13. Adryan B., and Teichmann S.A. FlyTF: A systematic review of site-specific transcription factors in the fruit fly drosophila melanogaster. Bioinformatics 22 (2006) 1532-1533
14. Riano-Pachon D.M., Ruzicic S., Dreyer I., and Mueller-Roeber B. PlnTFDB: An integrative plant transcription factor database. BMC Bioinformatics 8 (2007) 42
15. Kummerfeld S.K., and Teichmann S.A. DBD: A transcription factor prediction database. Nucleic Acids Res. 34 (2006) D74-D81
16. Aravind L., Anantharaman V., Balaji S., Babu M.M., and Iyer L.M. The many faces of the helix-turn-helix domain: Transcription regulation and beyond. FEMS Microbiol. Rev. 29 (2005) 231-262
17. Woese C.R., Kandler O., and Wheelis M.L. Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya. Proc. Natl. Acad. Sci. U. S. A. 87 (1990) 4576-4579
18. Bell S.D., and Jackson S.P. Transcription and translation in archaea: a mosaic of eukaryal and bacterial features. Trends Microbiol. 6 (1998) 222-228
19. Kyrpides N.C., and Ouzounis C.A. Transcription in archaea. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 8545-8550
20. Bell S.D., Magill C.P., and Jackson S.P. Basal and regulated transcription in archaea. Biochem. Soc. Trans. 29 (2001) 392-395
21. Edgar R.C. Muscle: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
22. Li L., Stoeckert Jr. C.J., and Roos D.S. OrthoMCL: Identification of ortholog groups for eukaryotic genomes. Genome Res. 13 (2003) 2178-2189
23. Howe K., Bateman A., and Durbin R. QuickTree: Building huge neighbour-joining trees of protein sequences. Bioinformatics 18 (2002) 1546-1547
24. Zmasek C.M., and Eddy S.R. ATV: Display and manipulation of annotated phylogenetic trees. Bioinformatics 17 (2001) 383-384
25. Kanehisa M., Goto S., Kawashima S., and Nakaya A. The kegg databases at genomenet. Nucleic Acids Res. 30 (2002) 42-46
26. Wu C.H., Apweiler R., Bairoch A., Natale D.A., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Mazumder R., O'Donovan C., Redaschi N., and Suzek B. The universal protein resource (uniprot): an expanding universe of protein information. Nucleic Acids Res. 34 (2006) D187-D191
27. Bateman A., Coin L., Durbin R., Finn R.D., Hollich V., Griffiths-Jones S., Khanna A., Marshall M., Moxon S., Sonnhammer E.L., Studholme D.J., Yeats C., and Eddy S.R. The pfam protein families database. Nucleic Acids Res. 32 (2004) D138-D141
28. Wilson D., Madera M., Vogel C., Chothia C., and Gough J. The superfamily database in 2007: families and functions. Nucleic Acids Res. 35 (2007) D308-D313
29. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped blast and psi-blast: A new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
30. Gollery M. Specialized hidden markov model databases for microbial genomics. Comp. Funct. Genomics 4 (2003) 250-254
31. Eddy S.R. Profile hidden markov models. Bioinformatics 14 (1998) 755-763
32. Madan Babu M., and Teichmann S.A. Evolution Of Transcription Factors And The Gene Regulatory Network In Escherichia Coli. Nucleic Acids Res. 31 (2003) 1234-1244