Nucleic Acids Research, 2001, Vol. 29, No. 1 281-283
© 2001 Oxford University Press
The TRANSFAC system on 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, 3BIOBASE GmbH, Mascheroder Weg 1B, D-38124 Braunschweig, Germany, and 4Technische Universität Braunschweig, Institut für Genetik–Biozentrum, Spielmannstraße 7, D-38106 Braunschweig, Germany
The TRANSFAC database on transcription factors and their DNA-binding sites and profiles (http://www.gene-regulation.de/) has been quantitatively extended and supplemented by a number of modules. These modules give information about pathologically relevant mutations in regulatory regions and transcription factor genes (PathoDB), scaffold/matrix attached regions (S/MARt DB), signal transduction (TRANSPATH) and gene expression sources (CYTOMER). Altogether, these distinct database modules constitute the TRANSFAC system. They are accompanied by a number of program routines for identifying potential transcription factor binding sites or for localizing individual components in the regulatory network of a cell.
* To whom correspondence should be addressed. Tel: +49 531 6181 427; Fax: +49 531 6181 266; Email: ewi{at}gbf.de
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 M. Shapira, E. Segal, and D. Botstein Disruption of Yeast Forkhead-associated Cell Cycle Transcription by Oxidative Stress Mol. Biol. Cell, December 1, 2004; 15(12): 5659 - 5669. [Abstract] [Full Text] [PDF]
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J. H. Kim and M. R. Stallcup Role of the Coiled-coil Coactivator (CoCoA) in Aryl Hydrocarbon Receptor-mediated Transcription J. Biol. Chem., November 26, 2004; 279(48): 49842 - 49848. [Abstract] [Full Text] [PDF]
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J. J. Welch, J. A. Watts, C. R. Vakoc, Y. Yao, H. Wang, R. C. Hardison, G. A. Blobel, L. A. Chodosh, and M. J. Weiss Global regulation of erythroid gene expression by transcription factor GATA-1 Blood, November 15, 2004; 104(10): 3136 - 3147. [Abstract] [Full Text] [PDF]
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L. Wang, A. Klopot, J.-N. Freund, L. N. Dowling, S. D. Krasinski, and J. C. Fleet Control of differentiation-induced calbindin-D9k gene expression in Caco-2 cells by cdx-2 and HNF-1{alpha} Am J Physiol Gastrointest Liver Physiol, November 1, 2004; 287(5): G943 - G953. [Abstract] [Full Text] [PDF]
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J. K. Divine, L. J. Staloch, H. Haveri, C. M. Jacobsen, D. B. Wilson, M. Heikinheimo, and T. C. Simon GATA-4, GATA-5, and GATA-6 activate the rat liver fatty acid binding protein gene in concert with HNF-1{alpha} Am J Physiol Gastrointest Liver Physiol, November 1, 2004; 287(5): G1086 - G1099. [Abstract] [Full Text] [PDF]
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 C. A. Wiwi, M. Gupte, and D. J. Waxman Sexually Dimorphic P450 Gene Expression in Liver-Specific Hepatocyte Nuclear Factor 4{alpha}-Deficient Mice Mol. Endocrinol., August 1, 2004; 18(8): 1975 - 1987. [Abstract] [Full Text] [PDF]
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 X. De Deken and M. Raymond Constitutive Activation of the PDR16 Promoter in a Candida albicans Azole-Resistant Clinical Isolate Overexpressing CDR1 and CDR2 Antimicrob. Agents Chemother., July 1, 2004; 48(7): 2700 - 2703. [Abstract] [Full Text] [PDF]
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 T. van Opijnen, J. Kamoschinski, R. E. Jeeninga, and B. Berkhout The Human Immunodeficiency Virus Type 1 Promoter Contains a CATA Box Instead of a TATA Box for Optimal Transcription and Replication J. Virol., July 1, 2004; 78(13): 6883 - 6890. [Abstract] [Full Text] [PDF]
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M. Kankainen and L. Holm POBO, transcription factor binding site verification with bootstrapping Nucleic Acids Res., July 1, 2004; 32(suppl_2): W222 - W229. [Abstract] [Full Text] [PDF]
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 H. Mayer, M. Bilban, V. Kurtev, F. Gruber, O. Wagner, B. R. Binder, and R. de Martin Deciphering Regulatory Patterns of Inflammatory Gene Expression From Interleukin-1--Stimulated Human Endothelial Cells Arterioscler Thromb Vasc Biol, July 1, 2004; 24(7): 1192 - 1198. [Abstract] [Full Text] [PDF]
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H. Yu, N. M. Luscombe, H. X. Lu, X. Zhu, Y. Xia, J.-D. J. Han, N. Bertin, S. Chung, M. Vidal, and M. Gerstein Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs Genome Res., June 1, 2004; 14(6): 1107 - 1118. [Abstract] [Full Text] [PDF]
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 S. MacArthur and J. F. Y. Brookfield Expected Rates and Modes of Evolution of Enhancer Sequences Mol. Biol. Evol., June 1, 2004; 21(6): 1064 - 1073. [Abstract] [Full Text] [PDF]
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J. W. Tullai, M. E. Schaffer, S. Mullenbrock, S. Kasif, and G. M. Cooper Identification of Transcription Factor Binding Sites Upstream of Human Genes Regulated by the Phosphatidylinositol 3-Kinase and MEK/ERK Signaling Pathways J. Biol. Chem., May 7, 2004; 279(19): 20167 - 20177. [Abstract] [Full Text] [PDF]
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S. Jorajuria, N. Dereuddre-Bosquet, K. Naissant-Storck, D. Dormont, and P. Clayette Differential Expression Levels of MRP1, MRP4, and MRP5 in Response to Human Immunodeficiency Virus Infection in Human Macrophages Antimicrob. Agents Chemother., May 1, 2004; 48(5): 1889 - 1891. [Abstract] [Full Text] [PDF]
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H.-D. Huang, J.-T. Horng, Y.-M. Sun, A.-P. Tsou, and S.-L. Huang Identifying transcriptional regulatory sites in the human genome using an integrated system Nucleic Acids Res., March 29, 2004; 32(6): 1948 - 1956. [Abstract] [Full Text] [PDF]
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H. R. Ueda, S. Hayashi, S. Matsuyama, T. Yomo, S. Hashimoto, S. A. Kay, J. B. Hogenesch, and M. Iino Universality and flexibility in gene expression from bacteria to human PNAS, March 16, 2004; 101(11): 3765 - 3769. [Abstract] [Full Text] [PDF]
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K. N. Maclean, E. Kraus, and J. P. Kraus The Dominant Role of Sp1 in Regulating the Cystathionine {beta}-Synthase -1a and -1b Promoters Facilitates Potential Tissue-specific Regulation by Kruppel-like Factors J. Biol. Chem., March 5, 2004; 279(10): 8558 - 8566. [Abstract] [Full Text] [PDF]
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