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P Stegmaier

Publications and source records attributed to P Stegmaier.

4 recordsLinked to original sources
PubMed2006

Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm.

Composite Module Analyst (CMA) is a novel software tool aiming to identify promoter-enhancer models based on the composition of transcription factor (TF) binding sites and their pairs. CMA is closely interconnected with the TRANSFAC database. In particular, CMA uses the positional weight matrix (PWM) library collected in TRANSFAC and therefore provides the possibility to search for a large variety of different TF binding sites. We model the structure of the long gene regulatory regions by a Boolean function that joins several local modules, each consisting of co-localized TF binding sites. Having as an input a set of co-regulated genes, CMA builds the promoter model and optimizes the parameters of the model automatically by applying a genetic-regression algorithm. We use a multicomponent fitness function of the algorithm which includes several statistical criteria in a weighted linear function. We show examples of successful application of CMA to a microarray data on transcription profiling of TNF-alpha stimulated primary human endothelial cells. The CMA web server is freely accessible at http://www.gene-regulation.com/pub/programs/cma/CMA.html. An advanced version of CMA is also a part of the commercial system ExPlaintrade mark (www.biobase.de) designed for causal analysis of gene expression data.

Algorithms↗
PubMed2006

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes.

The TRANSFAC database on transcription factors, their binding sites, nucleotide distribution matrices and regulated genes as well as the complementing database TRANSCompel on composite elements have been further enhanced on various levels. A new web interface with different search options and integrated versions of Match and Patch provides increased functionality for TRANSFAC. The list of databases which are linked to the common GENE table of TRANSFAC and TRANSCompel has been extended by: Ensembl, UniGene, EntrezGene, HumanPSD and TRANSPRO. Standard gene names from HGNC, MGI and RGD, are included for human, mouse and rat genes, respectively. With the help of InterProScan, Pfam, SMART and PROSITE domains are assigned automatically to the protein sequences of the transcription factors. TRANSCompel contains now, in addition to the COMPEL table, a separate table for detailed information on the experimental EVIDENCE on which the composite elements are based. Finally, for TRANSFAC, in respect of data growth, in particular the gain of Drosophila transcription factor binding sites (by courtesy of the Drosophila DNase I footprint database) and of Arabidopsis factors (by courtesy of DATF, Database of Arabidopsis Transcription Factors) has to be stressed. The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html.

Animals↗
PubMed2001

[Technical construction, calibration and results with a new intraocular pressure sensor with telemetric transmission].

BACKGROUND: Presently intraocular pressure is measured indirectly by applanation or impression of the cornea. Only isolated values are available with this method. We present a new implantable system for direct and continuos measurement of the intraocular pressure. METHODS: An implantable system consisting of a miniaturized sensor and a telemetric unit was integrated in an intraocular lens. The eye pressure is determined by the sensor, modulated and transduced by the telemetric system. By an extracorporal receiver the signal is demodulated. The electric supply of the intraocular system is achieved by external electromagnetic induction. RESULTS: The telemetric transmission of the intraocular pressure can be achieved with an accuracy of +/- 1 mm Hg and a frequency of registration of 3 values per second. CONCLUSION: Clinical application necessitates further animal trials in vivo.

Calibration↗