TFClass: An expandable hierarchical classification of human transcription factors

Nucleic Acids Research

Volumn 41, Issue D1, 2013, Pages

  Wingender, Edgar ^a,b   Schoeps, Torsten ^a   Dönitz, Jürgen ^a  

^a UNIVERSITY MEDICAL CENTER GÖTTINGEN   (Germany)

^b GeneXplain GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ALTERNATIVE RNA SPLICING; ARTICLE; BINDING AFFINITY; CLASSIFICATION ALGORITHM; GENE PRODUCT; HUMAN; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DNA BINDING; PROTEIN PROCESSING; SEARCH ENGINE;

DATABASES, PROTEIN; DNA-BINDING PROTEINS; HUMANS; INTERNET; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; TRANSCRIPTION FACTORS;

EID: 84876529769     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1123     Document Type: Article

References (31)

1. Carey, M. (1998) The enhanceosome and transcriptional synergy. Cell, 92, 5-8.
2. Kel-Margoulis, O.V., Kel, A.E., Reuter, I., Deineko, I.V. and Wingender, E. (2002) TRANSCompel: a database on composite regulatory elements in eukaryotic genes. Nucleic Acids Res., 30, 332-334.
3. Zaret, K.S. and Carroll, J.S. (2011) Pioneer transcription factors: establishing competence for gene expression. Genes Dev., 25, 2227-2241.
4. Mullen, A.C., Orlando, D.A., Newman, J.J., Loven, J., Kumar, R.M., Bilodeau, S., Reddy, J., Guenther, M.G., DeKoter, R.P. and Young, R.A. (2011) Master transcription factors determine cell-type-specific responses to TGF-b signaling. Cell, 147, 565-576.
5. Li, J., Hua, X., Haubrock, M., Wang, J. and Wingender, E. (2012) The architecture of the gene regulatory networks for different somatic cells. Bioinformatics, 28, i509-i514.
6. Suzuki, M. and Yagi, N. (1994) DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families. Proc. Natl Acad. Sci. USA, 91, 12357-12361.
7. Chu, W.Y., Huang, Y.F., Huang, C.C., Cheng, Y.S., Huang, C.K. and Oyang Y. J. (2009) ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors. Nucleic Acids Res., 37, W396-W401.
8. Harrison, S.C. (1991) A structural taxonomy of DNA-binding domains. Nature, 353, 715-719.
9. Vaquerizas, J.M., Kummerfeld, S.K., Teichmann, S.A. and Luscombe, N.M. (2009) A census of human transcription factors: function, expression and evolution. Nat. Rev. Genet., 10, 252-263.
10. 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.
11. Luscombe, N.M., Austin, S.E., Berman, H.M. and Thornton, J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol., 1, REVIEWS001.
12. Zhang, H.M., Chen, H., Liu, W., Liu, H., Gong, J., Wang, H. and Guo, A.Y. (2012) AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res., 40, D144-D119.
13. Fulton, D.L., Sundararajan, S., Badis, G., Hughes, T.R., Wasserman, W.W., Roach, J.C. and Sladek, R. (2009) TFCat: the curated catalog of mouse and human transcription factors. Genome Biol., 10, R29.
14. Wingender, E. (1988) Compilation of transcription regulating proteins. Nucleic Acids Res., 16, 1879-1902.
15. Matys, V., Kel-Margoulis, O.V., Fricke, E., Liebich, I., Land, S., Barre-Dirrie, A., Reuter, I., Chekmenev, D., Krull, M., Hornischer, K. et al. (2006) TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Res., 34, D108-D110.
16. Wingender, E. (2008) The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief. Bioinform., 9, 326-332.
17. Quandt, K., Frech, K., Karas, H., Wingender, E. and Werner, T. (1995) MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
18. Kel, A.E., Gossling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V. and Wingender, E. (2003) MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.
19. Wingender, E. (1997) Classification of eukaryotic transcription factors. Mol. Biol. Engl. Tr., 31, 483-497.
20. Heinemeyer, T., Chen, X., Karas, H., Kel, A.E., Kel, O.V., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F. and Wingender, E. (1999) Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms. Nucleic Acids Res., 27, 318-322.
21. UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
22. Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlic, A., Quesada, M., Quinn, G.B., Westbrook, J.D. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
23. Sievers, F., Wilm, A., Dineen, D.G., Gibson, T.J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Soding, J. et al. (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol., 7, 539.
24. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
25. Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24, 1596-1599.
26. Hagopian, R., Davidson, J.R., Datta, R.S., Samad, B., Jarvis, G.R. and Sjolander, K. (2010) SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction. Nucleic Acids Res., 38, W29-W34.
27. Donitz, J. and Wingender, E. (2012) The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications. Front. Genet., 3, 197.
28. Tipton, K. and Boyce, S. (2000) History of the enzyme nomenclature system. Bioinformatics, 16, 34-40.
29. Wingender, E. (1994) Recognition of regulatory regions in genomic sequences. J. Biotechnol., 35, 273-280.
30. Knuppel, R., Dietze, P., Lehnberg, W., Frech, K. and Wingender, E. (1994) TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins. J. Comput. Biol., 1, 191-198.
31. Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., Jonasson, K., Forsberg, M., Zwahlen, M., Kampf, C., Wester, K., Hober, S. et al. (2010) Towards a knowledge-based Human Protein Atlas. Nat. Biotechnol., 28, 1248-1250.