Bioinformatics Advance Access originally published online on April 28, 2005
Bioinformatics 2005 21(13):2933-2942; doi:10.1093/bioinformatics/bti473
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MatInspector and beyond: promoter analysis based on transcription factor binding sites
Genomatix Software GmbH Landsberger Strasse. 6, 80339 München, 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 (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, 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 TFBS 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).
Contact: cartharius{at}genomatix.de
Supplementary information: http://www.genomatix.de/matinspector.html
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 O. H. Kantarci, D. D. Hebrink, J. Schaefer-Klein, Y. Sun, S. Achenbach, E. J. Atkinson, S. Heggarty, A. C. Cotleur, M. de Andrade, K. Vandenbroeck, et al. Interferon Gamma Allelic Variants: Sex-Biased Multiple Sclerosis Susceptibility and Gene Expression Arch Neurol, March 1, 2008; 65(3): 349 - 357. [Abstract] [Full Text] [PDF]
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A. Saha, C. E. Hammond, M. Trojanowska, and A. J. Smolka Helicobacter pylori-induced H,K-ATPase {alpha}-subunit gene repression is mediated by NF-{kappa}B p50 homodimer promoter binding Am J Physiol Gastrointest Liver Physiol, March 1, 2008; 294(3): G795 - G807. [Abstract] [Full Text] [PDF]
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 M. C. Palmieri, S. Sell, X. Huang, M. Scherf, T. Werner, J. Durner, and C. Lindermayr Nitric oxide-responsive genes and promoters in Arabidopsis thaliana: a bioinformatics approach J. Exp. Bot., February 13, 2008; (2008) erm345v1. [Abstract] [Full Text] [PDF]
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S. Denger, T. Bahr-Ivacevic, H. Brand, G. Reid, J. Blake, M. Seifert, C.-Y. Lin, K. May, V. Benes, E. T. Liu, et al. Transcriptome Profiling of Estrogen-Regulated Genes in Human Primary Osteoblasts Reveals an Osteoblast-Specific Regulation of the Insulin-Like Growth Factor Binding Protein 4 Gene Mol. Endocrinol., February 1, 2008; 22(2): 361 - 379. [Abstract] [Full Text] [PDF]
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C. Gates Goodyer, Z. Rhani, and H. Zheng Expression of the Hepatic Specific V1 Messenger Ribonucleic Acid of the Human Growth Hormone Receptor Gene Is Regulated by Hepatic Nuclear Factor (HNF)-4{alpha}2 and HNF-4{alpha}8 Mol. Endocrinol., February 1, 2008; 22(2): 485 - 500. [Abstract] [Full Text] [PDF]
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 M. J. Corenblum, V. E. Wise, K. Georgi, B. D. Hammock, P. A. Doris, and M. Fornage Altered Soluble Epoxide Hydrolase Gene Expression and Function and Vascular Disease Risk in the Stroke-Prone Spontaneously Hypertensive Rat Hypertension, February 1, 2008; 51(2): 567 - 573. [Abstract] [Full Text] [PDF]
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W. Feng, J. Huang, J. Zhang, and T. Williams Identification and Analysis of a Conserved Tcfap2a Intronic Enhancer Element Required for Expression in Facial and Limb Bud Mesenchyme Mol. Cell. Biol., January 1, 2008; 28(1): 315 - 325. [Abstract] [Full Text] [PDF]
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R. Soundararajan, J. Wang, D. Melters, and D. Pearce Differential Activities of Glucocorticoid-induced Leucine Zipper Protein Isoforms J. Biol. Chem., December 14, 2007; 282(50): 36303 - 36313. [Abstract] [Full Text] [PDF]
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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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 E.L. Crawford, T. Blomquist, D.N. Mullins, Y. Yoon, D.R. Hernandez, M. Al-Bagdhadi, J. Ruiz, J. Hammersley, and J.C. Willey CEBPG regulates ERCC5/XPG expression in human bronchial epithelial cells and this regulation is modified by E2F1/YY1 interactions Carcinogenesis, December 1, 2007; 28(12): 2552 - 2559. [Abstract] [Full Text] [PDF]
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 M Bustamante, X Nogues, L Mellibovsky, L Agueda, S Jurado, E Caceres, J Blanch, R Carreras, A Diez-Perez, D Grinberg, et al. Polymorphisms in the interleukin-6 receptor gene are associated with bone mineral density and body mass index in Spanish postmenopausal women Eur. J. Endocrinol., November 1, 2007; 157(5): 677 - 684. [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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