Biomedical subjects

Claudia Choi

Publications and source records attributed to Claudia Choi.

8 recordsLinked to original sources

PubMed2007

SYSTOMONAS--an integrated database for systems biology analysis of Pseudomonas.

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 gene-regulatory networks were stored. Reconstruction of metabolic networks in SYSTOMONAS was achieved via comparative genomics. Broad data integration is realized using SOAP interfaces for the well established databases BRENDA, KEGG and PRODORIC. Several tools for the analysis of stored data and for the visualization of the corresponding results are provided, enabling a quick understanding of metabolic pathways, genomic arrangements or promoter structures of interest. The focus of SYSTOMONAS is on pseudomonads and in particular Pseudomonas aeruginosa, an opportunistic human pathogen. With this database we would like to encourage the Pseudomonas community to elucidate cellular processes of interest using an integrated systems biology strategy. The database is accessible at http://www.systomonas.de.

Bacterial Proteins↗

PubMed2006

JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.

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 well as the threshold value-independent Kolmogorov-Smirnov and Student's t-test were employed in order to identify the groups of genes with a significantly altered expression profile. Furthermore, we provide the application of the rank-based unpaired Wilcoxon's test for a GO-based microarray data interpretation. Further features of the program include recognition of the alternative gene names and the correction for multiple testing. Obtained results are visualized interactively both as a table and as a GO subgraph including all significant nodes. Currently, JProGO enables the analysis of microarray data from more than 20 different prokaryotic species, including all important model organisms, and thus constitutes a useful web service for the microbial research community. JProGO is freely accessible via the web at the following address: http://www.jprogo.de.

Archaea↗

PubMed2006

TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations.

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 their post-translational modifications. Reactions are similarly hierarchically organized in a three-layer architecture, differentiating between reactions that are evidenced by individual publications, generalizations of these reactions to construct species-independent 'reference pathways' and the 'semantic projections' of these pathways. A number of search and browse options allow easy access to the database contents, which can be visualized with the tool PathwayBuildertrade mark. The module PathoSign adds data about pathologically relevant mutations in signaling components, including their genotypes and phenotypes. TRANSPATH and PathoSign can be used as encyclopaedia, in the educational process, for vizualization and modeling of signal transduction networks and for the analysis of gene expression data. TRANSPATH Public 6.0 is freely accessible for users from non-profit organizations under http://www.gene-regulation.com/pub/databases.html.

Computer Graphics↗

PubMed2004

Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database.

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 multidimensional space of posttranslational modification, molecular family relationships, and the biological species of its origin. The new model makes the data better suitable for reconstructing signaling pathways and networks and mapping expression data, for instance from microarray experiments, onto regulatory networks.

Algorithms↗

PubMed2004

PathoPlant: a database on plant-pathogen interactions.

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. PathoPlant has been developed as a relational database to display relevant components and reactions involved in signal transduction related to plant-pathogen interactions. On the organism level, the tables 'plant', 'pathogen' and 'interaction' are used to describe incompatible interactions between plants and pathogens or diseases. On the molecular level, plant pathogenesis related information is organized in PathoPlant's main tables 'molecule', 'reaction' and 'location'. Signal transduction pathways are modeled as consecutive sequences of known molecules and corresponding reactions. PathoPlant entries are linked to associated internal records as well as to entries in external databases such as SWISS-PROT, GenBank, PubMed, and TRANSFAC. PathoPlant is available as a web-based service at http://www.pathoplant.de.

Computational Biology↗

PubMed2003

TRANSPATH: an integrated database on signal transduction and a tool for array analysis.

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 and their products, which may themselves be involved in regulatory action. As of July 2002, the TRANSPATH Professional release 3.2 contains about 9800 molecules, >1800 genes and >11 400 reactions collected from approximately 5000 references. With the ArrayAnalyzer, an integrated tool has been developed for evaluation of microarray data. It uses the TRANSPATH data set to identify key regulators in pathways connected with up- or down-regulated genes of the respective array. The key molecules and their surrounding networks can be viewed with the PathwayBuilder, a tool that offers four different modes of visualization. More information on TRANSPATH is available at http://www.biobase.de/pages/products/databases.html.

Animals↗

PubMed2002

The TGF-beta--Smad network: introducing bioinformatic tools.

The TGF-beta superfamily is an important class of intercellular signalling molecule, including TGF-beta and bone morphogenetic proteins. Intracellular signalling cascades triggered by these molecules eventually activate transcription factors of the Smad family, which then regulate expression of their respective target genes. This article will discuss the TGF-beta--Smad signalling networks and how these processes are represented in databases of signal transduction and transcription control mechanisms. These databases can provide a well-structured overview of the subject and a basis for advanced bioinformatics analyses to interpret the function of genomic sequences or to analyse signalling networks.

Animals↗

PubMed2002

Impact of polyphenols on growth of the aquatic herbivore Acentria ephemerella.

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. spicatum and whether this is due to polyphenols in their food source. Larvae originating from the same egg clutch grew faster and larger on P. perfoliatus than on M. spicatum. The same growth response was observed with larvae that spent winter diapause on either P. perfoliatus or M. spicatum. These larvae were fed either with their host plant or the other macrophyte. No prior feeding effect was found, but growth of larvae reared on M. spicatum was less than when grown on P. perfoliatus. Larvae from another egg-clutch reared on M. spicatum, either from lake or cultivated in aquaria, exhibited reduced growth on the lake plants. P. perfoliatus contained less than 1% and M. spicatum (aquarium or field material) between 5 and 9% phenolic compounds. No differences in nitrogen content of leaves were found, but apical shoot sections of M. spicatum exhibited a significantly higher nitrogen content than P. perfoliatus. Our results indicate that hydrolyzable tannins are responsible for the reduced growth of Acentria when fed with M. spicatum.

Animals↗