Bioinformatics Advance Access published online on April 28, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti473
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1 Genomatix Software GmbH, Munich, Germany
* To whom correspondence should be addressed.
Motivation: Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites with reasonable accuracy. Only with reliable predictions the next steps in promoter analysis can be tackled, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes. Results: We present a new version of the program MatInspector that identifies transcription factor binding sites in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper). Availability: MatInspector and the other programs described here can be used online at http://www.genomatix.de/matinspector.html. Access is free after registration within certain limitations (e.g. the number of analysis per month is currently limited to 20 analyses of arbitrary sequences). Supplementary Information:
Received March 14, 2005
Revised April 25, 2005
Accepted April 25, 2005
Article
MatInspector and beyond: promoter analysis based on transcription factor binding sites
K. Cartharius, E-mail: cartharius{at}genomatix.de
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J. C. Nwachukwu, W. Li, I. Pineda-Torra, H. Y. Huang, R. Ruoff, E. Shapiro, S. S. Taneja, S. K. Logan, and M. J. Garabedian Transcriptional Regulation of the Androgen Receptor Cofactor Androgen Receptor Trapped Clone-27 Mol. Endocrinol., December 1, 2007; 21(12): 2864 - 2876. [Abstract] [Full Text] [PDF]
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A. Henke, C. Marc Luetjens, M. Simoni, and J. Gromoll Chorionic Gonadotropin {beta}-Subunit Gene Expression in the Marmoset Pituitary Is Controlled by Steroidogenic Factor 1, Early Growth Response Protein 1, and Pituitary Homeobox Factor 1 Endocrinology, December 1, 2007; 148(12): 6062 - 6072. [Abstract] [Full Text] [PDF]
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B. P. Gomez, R. B. Riggins, A. N. Shajahan, U. Klimach, A. Wang, A. C. Crawford, Y. Zhu, A. Zwart, M. Wang, and R. Clarke Human X-Box binding protein-1 confers both estrogen independence and antiestrogen resistance in breast cancer cell lines FASEB J, December 1, 2007; 21(14): 4013 - 4027. [Abstract] [Full Text] [PDF]
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 M. L. Maeder, B. J. Polansky, B. E. Robson, and D. A. Eastman Phylogenetic Footprinting Analysis in the Upstream Regulatory Regions of the Drosophila Enhancer of split Genes Genetics, November 1, 2007; 177(3): 1377 - 1394. [Abstract] [Full Text] [PDF]
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V. T. Todorov, M. Desch, N. Schmitt-Nilson, A. Todorova, and A. Kurtz Peroxisome Proliferator-Activated Receptor-{gamma} Is Involved in the Control of Renin Gene Expression Hypertension, November 1, 2007; 50(5): 939 - 944. [Abstract] [Full Text] [PDF]
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R. Range, F. Lapraz, M. Quirin, S. Marro, L. Besnardeau, and T. Lepage Cis-regulatory analysis of nodal and maternal control of dorsal-ventral axis formation by Univin, a TGF-{beta} related to Vg1 Development, October 15, 2007; 134(20): 3649 - 3664. [Abstract] [Full Text] [PDF]
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B. Berarducci, M. Sommer, L. Zerboni, J. Rajamani, and A. M. Arvin Cellular and Viral Factors Regulate the Varicella-Zoster Virus gE Promoter during Viral Replication J. Virol., October 1, 2007; 81(19): 10258 - 10267. [Abstract] [Full Text] [PDF]
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 M. Barrachina, J. Moreno, S. Juves, D. Moreno, M. Olive, and I. Ferrer Target Genes of Neuron-Restrictive Silencer Factor Are Abnormally Up-Regulated in Human Myotilinopathy Am. J. Pathol., October 1, 2007; 171(4): 1312 - 1323. [Abstract] [Full Text] [PDF]
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 A. F. Keating, P. Davoren, T. J. Smith, R. P. Ross, and M. T. Cairns Bovine {kappa}-Casein Gene Promoter Haplotypes with Potential Implications for Milk Protein Expression J Dairy Sci, September 1, 2007; 90(9): 4092 - 4099. [Abstract] [Full Text] [PDF]
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A. Kanematsu, A. Ramachandran, and R. M. Adam GATA-6 mediates human bladder smooth muscle differentiation: involvement of a novel enhancer element in regulating {alpha}-smooth muscle actin gene expression Am J Physiol Cell Physiol, September 1, 2007; 293(3): C1093 - C1102. [Abstract] [Full Text] [PDF]
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N. Jonckheere, A. Vincent, M. Perrais, M.-P. Ducourouble, A. K.-v. Male, J.-P. Aubert, P. Pigny, K. L. Carraway, J.-N. Freund, I. B. Renes, et al. The Human Mucin MUC4 Is Transcriptionally Regulated by Caudal-related Homeobox, Hepatocyte Nuclear Factors, Forkhead Box A, and GATA Endodermal Transcription Factors in Epithelial Cancer Cells J. Biol. Chem., August 3, 2007; 282(31): 22638 - 22650. [Abstract] [Full Text] [PDF]
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D. J. Bolland, A. L. Wood, R. Afshar, K. Featherstone, E. M. Oltz, and A. E. Corcoran Antisense Intergenic Transcription Precedes Igh D-to-J Recombination and Is Controlled by the Intronic Enhancer E{micro} Mol. Cell. Biol., August 1, 2007; 27(15): 5523 - 5533. [Abstract] [Full Text] [PDF]
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 J. Dumont, M. Zureik, D. Cottel, M. Montaye, P. Ducimetiere, P. Amouyel, and T. Brousseau Association of arginase 1 gene polymorphisms with the risk of myocardial infarction and common carotid intima media thickness J. Med. Genet., August 1, 2007; 44(8): 526 - 531. [Abstract] [Full Text] [PDF]
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J.-P. Segain, M. Rolli-Derkinderen, N. Gervois, D. Raingeard de la Bletiere, G. Loirand, and P. Pacaud Urotensin II is a New Chemotactic Factor for UT Receptor-Expressing Monocytes J. Immunol., July 15, 2007; 179(2): 901 - 909. [Abstract] [Full Text] [PDF]
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 N. A. Kolchanov, T. I. Merkulova, E. V. Ignatieva, E. A. Ananko, D. Yu. Oshchepkov, V. G. Levitsky, G. V. Vasiliev, N. V. Klimova, V. M. Merkulov, and T. C. Hodgman Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes Brief Bioinform, July 12, 2007; (2007) bbm027v1. [Abstract] [Full Text] [PDF]
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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]
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 N. Jayasundara, D. W. Towle, D. Weihrauch, and C. Spanings-Pierrot Gill-specific transcriptional regulation of Na+/K+-ATPase {alpha}-subunit in the euryhaline shore crab Pachygrapsus marmoratus: sequence variants and promoter structure J. Exp. Biol., June 15, 2007; 210(12): 2070 - 2081. [Abstract] [Full Text] [PDF]
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M. Severa, M. E. Remoli, E. Giacomini, V. Annibali, V. Gafa, R. Lande, M. Tomai, M. Salvetti, and E. M. Coccia Sensitization to TLR7 Agonist in IFN-beta-Preactivated Dendritic Cells J. Immunol., May 15, 2007; 178(10): 6208 - 6216. [Abstract] [Full Text] [PDF]
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L. Li, Y. Liang, and R. L. Bass GAPWM: a genetic algorithm method for optimizing a position weight matrix Bioinformatics, May 15, 2007; 23(10): 1188 - 1194. [Abstract] [Full Text] [PDF]
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X. Li, B. B. Madison, W. Zacharias, A. Kolterud, D. States, and D. L. Gumucio Deconvoluting the intestine: molecular evidence for a major role of the mesenchyme in the modulation of signaling cross talk Physiol Genomics, May 11, 2007; 29(3): 290 - 301. [Abstract] [Full Text] [PDF]
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