Nucleic Acids Research, 2000, Vol. 28, No. 1 316-319
© 2000 Oxford University Press
TRANSFAC: an integrated system for gene expression regulation
1Gesellschaft für Biotechnologische Forschung mbH, Mascheroder Weg 1, D-38124 Braunschweig, Germany, 2The National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, People’s Republic of China, 3Technische Universität Braunschweig, Biozentrum, D-39100 Braunschweig, Germany and 4BIOBASE GmbH, Mascheroder Weg 1B, D-38124 Braunschweig, Germany
TRANSFAC is a database on transcription factors, their genomic binding sites and DNA-binding profiles (http://transfac.gbf.de/TRANSFAC/ ). Its content has been enhanced, in particular by information about training sequences used for the construction of nucleotide matrices as well as by data on plant sites and factors. Moreover, TRANSFAC has been extended by two new modules: PathoDB provides data on pathologically relevant mutations in regulatory regions and transcription factor genes, whereas S/MARt DB compiles features of scaffold/matrix attached regions (S/MARs) and the proteins binding to them. Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources.
* To whom correspondence should be addressed. Tel: +49 531 6181 427; Fax: +49 531 6181 266; Email: ewi@gbf.de
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Y. Xu, S. A. Cei, A. Rodriguez Huete, K. S. Colletti, and G. S. Pari Human Cytomegalovirus DNA Replication Requires Transcriptional Activation via an IE2- and UL84-Responsive Bidirectional Promoter Element within oriLyt J. Virol., November 1, 2004; 78(21): 11664 - 11677. [Abstract] [Full Text] [PDF]
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M. Yang, J. Hay, and W. T. Ruyechan The DNA Element Controlling Expression of the Varicella-Zoster Virus Open Reading Frame 28 and 29 Genes Consists of Two Divergent Unidirectional Promoters Which Have a Common USF Site J. Virol., October 15, 2004; 78(20): 10939 - 10952. [Abstract] [Full Text] [PDF]
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 M. Cattaruzza, T. J. Guzik, W. Slodowski, A. Pelvan, J. Becker, M. Halle, A. B. Buchwald, K. M. Channon, and M. Hecker Shear Stress Insensitivity of Endothelial Nitric Oxide Synthase Expression as a Genetic Risk Factor for Coronary Heart Disease Circ. Res., October 15, 2004; 95(8): 841 - 847. [Abstract] [Full Text] [PDF]
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D. N. Messina, J. Glasscock, W. Gish, and M. Lovett An ORFeome-based Analysis of Human Transcription Factor Genes and the Construction of a Microarray to Interrogate Their Expression Genome Res., October 1, 2004; 14(10b): 2041 - 2047. [Abstract] [Full Text] [PDF]
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R. J. Livingston, A. von Niederhausern, A. G. Jegga, D. C. Crawford, C. S. Carlson, M. J. Rieder, S. Gowrisankar, B. J. Aronow, R. B. Weiss, and D. A. Nickerson Pattern of Sequence Variation Across 213 Environmental Response Genes Genome Res., October 1, 2004; 14(10a): 1821 - 1831. [Abstract] [Full Text] [PDF]
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 H. Staiger, S. Kaltenbach, K. Staiger, N. Stefan, A. Fritsche, A. Guirguis, C. Peterfi, M. Weisser, F. Machicao, M. Stumvoll, et al. Expression of Adiponectin Receptor mRNA in Human Skeletal Muscle Cells Is Related to In Vivo Parameters of Glucose and Lipid Metabolism Diabetes, September 1, 2004; 53(9): 2195 - 2201. [Abstract] [Full Text] [PDF]
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 F. Campagne, S. Neves, C.-w. Chang, L. Skrabanek, P. T. Ram, R. Iyengar, and H. Weinstein Quantitative Information Management for the Biochemical Computation of Cellular Networks Sci. Signal., August 31, 2004; 2004(248): pl11 - pl11. [Abstract] [Full Text] [PDF]
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Y. V. Sun, D. R. Boverhof, L. D. Burgoon, M. R. Fielden, and T. R. Zacharewski Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences Nucleic Acids Res., August 24, 2004; 32(15): 4512 - 4523. [Abstract] [Full Text] [PDF]
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Q. Zhou and W. H. Wong CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling PNAS, August 17, 2004; 101(33): 12114 - 12119. [Abstract] [Full Text] [PDF]
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 S. R. Kappeler, C. Heuberger, Z. Farah, and Z. Puhan Expression of the Peptidoglycan Recognition Protein, PGRP, in the Lactating Mammary Gland J Dairy Sci, August 1, 2004; 87(8): 2660 - 2668. [Abstract] [Full Text] [PDF]
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E. P. Xing and R. M. Karp MotifPrototyper: A Bayesian profile model for motif families PNAS, July 20, 2004; 101(29): 10523 - 10528. [Abstract] [Full Text] [PDF]
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A. Matyash, H.-R. Chung, and H. Jackle Genome-wide Mapping of in Vivo Targets of the Drosophila Transcription Factor Kruppel J. Biol. Chem., July 16, 2004; 279(29): 30689 - 30696. [Abstract] [Full Text] [PDF]
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 D. M. Barrett, K. S. Gustafson, J. Wang, S. Z. Wang, and G. D. Ginder A GATA Factor Mediates Cell Type-Restricted Induction of HLA-E Gene Transcription by Gamma Interferon Mol. Cell. Biol., July 15, 2004; 24(14): 6194 - 6204. [Abstract] [Full Text] [PDF]
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P. M. Haverty, M. C. Frith, and Z. Weng CARRIE web service: automated transcriptional regulatory network inference and interactive analysis Nucleic Acids Res., July 1, 2004; 32(suppl_2): W213 - W216. [Abstract] [Full Text] [PDF]
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L. Conde, J. M. Vaquerizas, J. Santoyo, F. Al-Shahrour, S. Ruiz-Llorente, M. Robledo, and J. Dopazo PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level Nucleic Acids Res., July 1, 2004; 32(suppl_2): W242 - W248. [Abstract] [Full Text] [PDF]
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R. Sharan, A. Ben-Hur, G. G. Loots, and I. Ovcharenko CREME: Cis-Regulatory Module Explorer for the human genome Nucleic Acids Res., July 1, 2004; 32(suppl_2): W253 - W256. [Abstract] [Full Text] [PDF]
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 M.-L. Asselin-Labat, M. David, A. Biola-Vidamment, D. Lecoeuche, M.-C. Zennaro, J. Bertoglio, and M. Pallardy GILZ, a new target for the transcription factor FoxO3, protects T lymphocytes from interleukin-2 withdrawal-induced apoptosis Blood, July 1, 2004; 104(1): 215 - 223. [Abstract] [Full Text] [PDF]
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