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TRANSPATH is a database system about gene regulatory networks that combines encyclopedic information on signal transduction with tools for visualization and analysis. The integration with TRANSFAC, a database about transcription factors and their DNA binding sites, provides the possibility to obtain complete signaling pathways from ligand to target genes(More)
TRANSPATH is a database about signal transduction events. It provides information about signaling molecules, their reactions and the pathways these reactions constitute. The representation of signaling molecules is organized in a number of orthogonal hierarchies reflecting the classification of the molecules, their species-specific or generic features, and(More)
UNLABELLED TRANSPATH is an information system on gene-regulatory pathways, and an extension module to the TRANSFAC database system (Wingender et al., Nucleic Acids Res., 28, 316-319, 2000). It focuses on pathways involved in the regulation of transcription factors in different species, mainly human, mouse and rat. Elements of the relevant signal(More)
Seasonal changes in the abundance of the herbivorous moth larvae Acentria ephemere/la on submersed macrophytes in Lake Constance were studied between 1998 and 2000. Acentria were found feeding on many pondweeds (Potamogeton lucens, P. pectinatus, P. perfoliatus), Ceratophyllum demersum and Myriophyllum spicatum, but not on Chara spp., Najas marina ssp.(More)
Larvae of Acentria ephemerella live fully submerged, feeding on submersed aquatic angiosperms such as pondweeds (Potamogeton spp.) and Myriophyllum spicatum. Only the latter contains high concentrations of hydrolyzable tannins known to interfere with the growth of insect herbivores. We tested whether larvae grow faster on Potamogeton perfoliatus or M.(More)
TRANSPATH can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyser. Therefore, three modules have been created: the first one is the data, which have been manually extracted, mostly from the primary literature; the second is PathwayBuilder, which provides several different(More)
To provide an integrated bioinformatics platform for a systems biology approach to the biology of pseudomonads in infection and biotechnology the database SYSTOMONAS (SYSTems biology of pseudOMONAS) was established. Besides our own experimental metabolome, proteome and transcriptome data, various additional predictions of cellular processes, such as(More)
The data model of the signaling pathways database TRANSPATH has been re-engineered to a three-layer model comprising experimental evidences and summarized pathway information, both in a mechanistically detailed manner, and a "semantic" projection for the abstract overview. Each molecule is described in the context of a certain reaction in the(More)
Pathogen recognition and signal transduction during plant pathogenesis is essential for the activation of plant defense mechanisms. To facilitate easy access to published data and to permit comparative studies of different pathogen response pathways, a database is indispensable to give a broad overview of the components and reactions so far known.(More)
A novel program suite was implemented for the functional interpretation of high-throughput gene expression data based on the identification of Gene Ontology (GO) nodes. The focus of the analysis lies on the interpretation of microarray data from prokaryotes. The three well established statistical methods of the threshold value-based Fisher's exact test, as(More)