Nucleic Acids Research, 2003, Vol. 31, No. 1 374-378
© 2003 Oxford University Press
TRANSFAC®: transcriptional regulation, from patterns to profiles
1 BIOBASE GmbH, Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany 2 Institut für Genetik-Biozentrum, Technische Universität Braunschweig, Spielmannstrasse. 7, D-38106 Braunschweig, Germany 3 Gesellschaft für Biotechnologische Forschung mbH, Mascheroder Weg 1, D-38124 Braunschweig, Germany
*To whom correspondence should be addressed. Email: vma{at}biobase.de
ABSTRACT
The TRANSFAC® database on eukaryotic transcriptional regulation, comprising data on transcription factors, their target genes and regulatory binding sites, has been extended and further developed, both in number of entries and in the scope and structure of the collected data. Structured fields for expression patterns have been introduced for transcription factors from human and mouse, using the CYTOMER® database on anatomical structures and developmental stages. The functionality of MatchTM, a tool for matrix-based search of transcription factor binding sites, has been enhanced. For instance, the program now comes along with a number of tissue-(or state-)specific profiles and new profiles can be created and modified with MatchTM Profiler. The GENE table was extended and gained in importance, containing amongst others links to LocusLink, RefSeq and OMIM now. Further, (direct) links between factor and target gene on one hand and between gene and encoded factor on the other hand were introduced. The TRANSFAC® public release is available at http://www.gene-regulation.com. For yeast an additional release including the latest data was made available separately as TRANSFAC® Saccharomyces Module (TSM) at http://transfac.gbf.de. For CYTOMER® free download versions are available at http://www.biobase.de:8080/index.html.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  J. Hu, H. Hu, and X. Li MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs Nucleic Acids Res., August 1, 2008; 36(13): 4488 - 4497. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K.-J. Won, A. Sandelin, T. T. Marstrand, and A. Krogh Modeling promoter grammars with evolving hidden Markov models Bioinformatics, August 1, 2008; 24(15): 1669 - 1675. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. H. Choi, Z. Rapti, V. Gelev, M. R. Hacker, B. Alexandrov, E. J. Park, J. S. Park, N. Horikoshi, A. Smerzi, K. O. Rasmussen, et al. Profiling the Thermodynamic Softness of Adenoviral Promoters Biophys. J., July 15, 2008; 95(2): 597 - 608. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Q. Zhou and J. S. Liu Extracting sequence features to predict protein-DNA interactions: a comparative study Nucleic Acids Res., July 1, 2008; 36(12): 4137 - 4148. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. L. Khan, R. Vadigepalli, M. K. McDonald, R. F. Rogers, G. R. Gao, and J. S. Schwaber Dynamic transcriptomic response to acute hypertension in the nucleus tractus solitarius Am J Physiol Regulatory Integrative Comp Physiol, July 1, 2008; 295(1): R15 - R27. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
B. Hooghe, P. Hulpiau, F. van Roy, and P. De Bleser ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species Nucleic Acids Res., July 1, 2008; 36(suppl_2): W128 - W132. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Smeenk, S. J. van Heeringen, M. Koeppel, M. A. van Driel, S. J. J. Bartels, R. C. Akkers, S. Denissov, H. G. Stunnenberg, and M. Lohrum Characterization of genome-wide p53-binding sites upon stress response Nucleic Acids Res., June 1, 2008; 36(11): 3639 - 3654. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. M. Whittington, A. T. Papenfuss, P. Bansal, A. M. Torres, E. S.W. Wong, J. E. Deakin, T. Graves, A. Alsop, K. Schatzkamer, C. Kremitzki, et al. Defensins and the convergent evolution of platypus and reptile venom genes Genome Res., June 1, 2008; 18(6): 986 - 994. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Galanter, S. Choudhry, C. Eng, S. Nazario, J. R. Rodriguez-Santana, J. Casal, A. Torres-Palacios, J. Salas, R. Chapela, H. G. Watson, et al. ORMDL3 Gene Is Associated with Asthma in Three Ethnically Diverse Populations Am. J. Respir. Crit. Care Med., June 1, 2008; 177(11): 1194 - 1200. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Hackenberg and R. Matthiesen Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists Bioinformatics, June 1, 2008; 24(11): 1386 - 1393. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Cai, C.-H. Li, A.-S. Xiong, R.-H. Peng, J. Zhou, F. Gao, Z. Zhang, and Q.-H. Yao DGTF: A Database of Grape Transcription Factors J. Amer. Soc. Hort. Sci., May 1, 2008; 133(3): 459 - 461. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. Tharakaraman, O. Bodenreider, D. Landsman, J. L. Spouge, and L. Marino-Ramirez The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site Nucleic Acids Res., May 1, 2008; 36(8): 2777 - 2786. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Chen, L. Guo, Z. Fan, and T. Jiang W-AlignACE: an improved Gibbs sampling algorithm based on more accurate position weight matrices learned from sequence and gene expression/ChIP-chip data Bioinformatics, May 1, 2008; 24(9): 1121 - 1128. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Yu, A. J. Mohamed, O. E. Simonson, L. Vargas, K. E. M. Blomberg, B. Bjorkstrand, H. J. Arteaga, B. F. Nore, and C. I. E. Smith Proteasome-dependent autoregulation of Bruton tyrosine kinase (Btk) promoter via NF-{kappa}B Blood, May 1, 2008; 111(9): 4617 - 4626. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C.-Q. Lai, K. L. Tucker, L. D. Parnell, X. Adiconis, B. Garcia-Bailo, J. Griffith, M. Meydani, and J. M. Ordovas PPARGC1A Variation Associated With DNA Damage, Diabetes, and Cardiovascular Diseases: The Boston Puerto Rican Health Study Diabetes, April 1, 2008; 57(4): 809 - 816. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Li, J. Wakefield, and S. Self A transdimensional Bayesian model for pattern recognition in DNA sequences Biostat., March 18, 2008; (2008) kxm058v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Roca and R. T. Franceschi Analysis of transcription factor interactions in osteoblasts using competitive chromatin immunoprecipitation Nucleic Acids Res., March 1, 2008; 36(5): 1723 - 1730. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. R. Sedaghat, J. German, T. M. Teslovich, J. Cofrancesco Jr., C. C. Jie, C. C. Talbot Jr., and R. F. Siliciano Chronic CD4+ T-Cell Activation and Depletion in Human Immunodeficiency Virus Type 1 Infection: Type I Interferon-Mediated Disruption of T-Cell Dynamics J. Virol., February 15, 2008; 82(4): 1870 - 1883. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Levy, D. Tatomer, C. B. Herber, X. Zhao, H. Tang, T. Sargeant, L. J. Ball, J. Summers, T. P. Speed, and D. C. Leitman Differential Regulation of Native Estrogen Receptor-Regulatory Elements by Estradiol, Tamoxifen, and Raloxifene Mol. Endocrinol., February 1, 2008; 22(2): 287 - 303. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
U. J. Pape, S. Rahmann, and M. Vingron Natural similarity measures between position frequency matrices with an application to clustering Bioinformatics, February 1, 2008; 24(3): 350 - 357. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. Cordero, M. Botta, and R. A. Calogero Microarray data analysis and mining approaches Brief Funct Genomic Proteomic, January 22, 2008; (2008) elm034v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. M. Gow, L. W. Chinn, and D. L. Kroetz The Effects of ABCB1 3'-Untranslated Region Variants on mRNA Stability Drug Metab. Dispos., January 1, 2008; 36(1): 10 - 15. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Xu, Y. Zhao, and R. Simon Gene Set Expression Comparison kit for BRB-ArrayTools Bioinformatics, January 1, 2008; 24(1): 137 - 139. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. G. Romero, M. W. Plonczynski, B. L. Welsh, C. E. Gomez-Sanchez, M. Y. Zhou, and E. P. Gomez-Sanchez Gene expression profile in rat adrenal zona glomerulosa cells stimulated with aldosterone secretagogues Physiol Genomics, December 19, 2007; 32(1): 117 - 127. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. S. Adler, S. Sinha, T. L.A. Kawahara, J. Y. Zhang, E. Segal, and H. Y. Chang Motif module map reveals enforcement of aging by continual NF-{kappa}B activity Genes & Dev., December 15, 2007; 21(24): 3244 - 3257. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Kheradpour, A. Stark, S. Roy, and M. Kellis Reliable prediction of regulator targets using 12 Drosophila genomes Genome Res., December 1, 2007; 17(12): 1919 - 1931. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. Meng, A. Banerjee, and L. Zhou BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences Bioinformatics, December 1, 2007; 23(23): 3249 - 3250. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 F. E. Lovegrove, S. A. Gharib, S. N. Patel, C. A. Hawkes, K. C. Kain, and W. C. Liles Expression Microarray Analysis Implicates Apoptosis and Interferon-Responsive Mechanisms in Susceptibility to Experimental Cerebral Malaria Am. J. Pathol., December 1, 2007; 171(6): 1894 - 1903. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. J. G. Post, M. Roos, M. S. Marshall, R. van Driel, and T. M. Breit A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data Bioinformatics, November 15, 2007; 23(22): 3080 - 3087. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. K. Saini, S. Griffiths-Jones, and A. J. Enright Genomic analysis of human microRNA transcripts PNAS, November 6, 2007; 104(45): 17719 - 17724. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. M. Keller, S. McWeeney, A. Arsenlis, J. Drouin, C. V. E. Wright, H. Wang, C. B. Wollheim, P. White, K. H. Kaestner, and R. H. Goodman Characterization of Pancreatic Transcription Factor Pdx-1 Binding Sites Using Promoter Microarray and Serial Analysis of Chromatin Occupancy J. Biol. Chem., November 2, 2007; 282(44): 32084 - 32092. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. R. Davies, L.-W. Chang, D. Patra, X. Xing, K. Posey, J. Hecht, G. D. Stormo, and L. J. Sandell Computational identification and functional validation of regulatory motifs in cartilage-expressed genes Genome Res., October 1, 2007; 17(10): 1438 - 1447. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. Lapointe, C. Li, C. P. Giacomini, K. Salari, S. Huang, P. Wang, M. Ferrari, T. Hernandez-Boussard, J. D. Brooks, and J. R. Pollack Genomic Profiling Reveals Alternative Genetic Pathways of Prostate Tumorigenesis Cancer Res., September 15, 2007; 67(18): 8504 - 8510. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. C M Brinkman-Van der Linden, N. Hurtado-Ziola, T. Hayakawa, L. Wiggleton, K. Benirschke, A. Varki, and N. Varki Human-specific expression of Siglec-6 in the placenta Glycobiology, September 1, 2007; 17(9): 922 - 931. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Kedmi and A. Orr-Urtreger Expression changes in mouse brains following nicotine-induced seizures: the modulation of transcription factor networks Physiol Genomics, August 20, 2007; 30(3): 242 - 252. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. C. Bolton, A. Y. So, C. Chaivorapol, C. M. Haqq, H. Li, and K. R. Yamamoto Cell- and gene-specific regulation of primary target genes by the androgen receptor Genes & Dev., August 15, 2007; 21(16): 2005 - 2017. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Guo, Y. Li, X. Gong, C. Yao, W. Ma, D. Wang, Y. Li, J. Zhu, M. Zhang, D. Yang, et al. Edge-based scoring and searching method for identifying condition-responsive protein protein interaction sub-network Bioinformatics, August 15, 2007; 23(16): 2121 - 2128. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L. Hertzberg, S. Izraeli, and E. Domany STOP: searching for transcription factor motifs using gene expression Bioinformatics, July 15, 2007; 23(14): 1737 - 1743. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Mahony and P. V. Benos STAMP: a web tool for exploring DNA-binding motif similarities Nucleic Acids Res., July 13, 2007; 35(suppl_2): W253 - W258. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
L.-W. Chang, B. R. Fontaine, G. D. Stormo, and R. Nagarajan PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis Nucleic Acids Res., July 13, 2007; 35(suppl_2): W238 - W244. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. A. Romer, G.-R. Kayombya, and E. Fraenkel WebMOTIFS: automated discovery, filtering and scoring of DNA sequence motifs using multiple programs and Bayesian approaches Nucleic Acids Res., July 13, 2007; 35(suppl_2): W217 - W220. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. Mahony, P. E. Auron, and P. V. Benos Inferring protein DNA dependencies using motif alignments and mutual information Bioinformatics, July 1, 2007; 23(13): i297 - i304. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. R. Kiela, N. Kuscuoglu, A. J. Midura, M. T. Midura-Kiela, C. B. Larmonier, M. Lipko, and F. K. Ghishan Molecular mechanism of rat NHE3 gene promoter regulation by sodium butyrate Am J Physiol Cell Physiol, July 1, 2007; 293(1): C64 - C74. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Bao, J. L. Peirce, M. Zhou, H. Li, D. Goldowitz, R. W. Williams, L. Lu, and Y. Cui An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes Hum. Mol. Genet., June 1, 2007; 16(11): 1381 - 1390. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Y. Sakakibara, T. Irie, Y. Suzuki, R. Yamashita, H. Wakaguri, A. Kanai, J. Chiba, T. Takagi, J. Mizushima-Sugano, S.-i. Hashimoto, et al. Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome DNA Res, May 23, 2007; (2007) dsm006v1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. B. Lowe, G. Bejerano, and D. Haussler Thousands of human mobile element fragments undergo strong purifying selection near developmental genes PNAS, May 8, 2007; 104(19): 8005 - 8010. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 D. Menendez, A. Inga, J. Snipe, O. Krysiak, G. Schonfelder, and M. A. Resnick A Single-Nucleotide Polymorphism in a Half-Binding Site Creates p53 and Estrogen Receptor Control of Vascular Endothelial Growth Factor Receptor 1 Mol. Cell. Biol., April 1, 2007; 27(7): 2590 - 2600. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. Kulshreshtha, M. Ferracin, S. E. Wojcik, R. Garzon, H. Alder, F. J. Agosto-Perez, R. Davuluri, C.-G. Liu, C. M. Croce, M. Negrini, et al. A MicroRNA Signature of Hypoxia Mol. Cell. Biol., March 1, 2007; 27(5): 1859 - 1867. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. Gat-Viks and R. Shamir Refinement and expansion of signaling pathways: The osmotic response network in yeast Genome Res., March 1, 2007; 17(3): 358 - 367. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Zhao, L. A. Schriefer, and G. D. Stormo Identification of muscle-specific regulatory modules in Caenorhabditis elegans Genome Res., March 1, 2007; 17(3): 348 - 357. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 G. Amoutzias, A. Veron, J Weiner III, M Robinson-Rechavi, E Bornberg-Bauer, S. Oliver, and D. Robertson One Billion Years of bZIP Transcription Factor Evolution: Conservation and Change in Dimerization and DNA-Binding Site Specificity Mol. Biol. Evol., March 1, 2007; 24(3): 827 - 835. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. W. Siggers and B. Honig Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry Nucleic Acids Res., February 28, 2007; 35(4): 1085 - 1097. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Frickey and G. Weiller Mclip: motif detection based on cliques of gapped local profile-to-profile alignments Bioinformatics, February 15, 2007; 23(4): 502 - 503. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Donn, A. Berry, A. Stevens, S. Farrow, J. Betts, R. Stevens, C. Clayton, J. Wang, L. Warnock, J. Worthington, et al. Use of gene expression profiling to identify a novel glucocorticoid sensitivity determining gene, BMPRII FASEB J, February 1, 2007; 21(2): 402 - 414. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. S. Bais, S. Grossmann, and M. Vingron Simultaneous alignment and annotation of cis-regulatory regions Bioinformatics, January 15, 2007; 23(2): e44 - e49. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. G. Roider, A. Kanhere, T. Manke, and M. Vingron Predicting transcription factor affinities to DNA from a biophysical model Bioinformatics, January 15, 2007; 23(2): 134 - 141. [Abstract] [Full Text] [PDF]
|
|