MatInspector and beyond: promoter analysis based on transcription factor binding sites
Top Cited Papers
- 28 April 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Bioinformatics
- Vol. 21 (13), 2933-2942
- https://doi.org/10.1093/bioinformatics/bti473
Abstract
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@genomatix.de Supplementary information: http://www.genomatix.de/matinspector.htmlKeywords
This publication has 44 references indexed in Scilit:
- Targeted transcriptional repression of Gfi1 by GFI1 and GFI1B in lymphoid cellsNucleic Acids Research, 2004
- CONREAL: Conserved Regulatory Elements Anchored Alignment Algorithm for Identification of Transcription Factor Binding Sites by Phylogenetic FootprintingGenome Research, 2003
- Physical Interaction of the Activator Protein-1 Factors c-Fos and c-Jun with Cbfa1 for Collagenase-3 Promoter ActivationPublished by Elsevier BV ,2002
- Role of Cbfa1 in Ameloblastin Gene TranscriptionOnline Journal of Public Health Informatics, 2001
- Transcriptional regulation of galectin-10 (eosinophil Charcot-Leyden crystal protein): A GC box (−44 to −50) controls butyric acid induction of gene expressionLife Sciences, 2001
- ATF and Jun transcription factors, acting through an Ets / CRE promoter module, mediate lipopolysaccharide inducibility of the chemokine RANTES in monocytic Mono Mac 6 cellsEuropean Journal of Immunology, 2000
- Improved ballistic transient transformation conditions for tomato fruit allow identification of organ‐specific contributions of I‐box and G‐box to the RBCS2 promoter activityThe Plant Journal, 1997
- Rat Osteoblast and Osteosarcoma Nuclear Matrix Proteins Bind with Sequence Specificity to the Rat Type I Collagen PromoterEndocrinology, 1997
- MATRIX SEARCH 1.0: a computer program that scans DNA sequences for transcriptional elements using a database of weight matricesBioinformatics, 1995
- Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequencesJournal of Molecular Biology, 1990