TRANSPATH(R): an integrated database on signal transduction and a tool for array analysis

Abstract

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.

Modulation of the TLR-Mediated Inflammatory Response by the Endogenous Human Host Defense Peptide LL-37

“…Furthermore, the gene expression data was overlaid on molecular interaction networks using Cytoscape (32). Interactions networks were custom-built from manually curated data and information contained within the Transpath pathway database (33). Differentially expressed genes with similar temporal expression profiles were clustered using the partitioning algorithm K-means procedure (as implemented in TIGR's Multiple Experiment Viewer), with each cluster representing a set of potential coregulated genes (based on their similar expression profiles over time), although the number of time points used prevents highly precise predictions.…”

TRANSPATH®—a high quality database focused on signal transduction

“…We segmented signal transduction into three major functional units: signalling components called 'molecules', interactions connecting these molecules called 'reactions', and 'genes' to differentiate transcriptional regulation of genes and protein interactions [8]. They are connected by a bipartite directed graph, the nodes alternately representing molecules and reactions, genes being treated as a subset of molecules.…”

“…With the aim of achieving more reliable data, several interaction databases have been initiated, such as DIP [18], BIND [1] and aMAZE [16], where interactions have been inferred mostly by high-throughput experiments and mainly on yeast species. Databases concentrating more on human or mammalian proteins are CSNDB [14], TRANSPATH  [6,8,13] and MINT [19]. Among these, TRANSPATH  seems to contain the highest number of mammalian data points, in relative terms as well as in absolute numbers: over 72% of all so-called 'basic' molecules are mammalian proteins, of which about 2400 are human molecules (see Figure 1).…”

Identifying Transcription Factors and microRNAs as Key Regulators of Pathways Using Bayesian Inference on Known Pathway Structures

“…In order to facilitate the elucidation of these regulatory mechanisms, several databases have been released based on the analysis of sequence information for predicted regulatory interactions. Backes et al [2] have compiled a dictionary on microRNAs and their putative pathways based on the enrichment of the predicted microRNAs targets for each pathway in KEGG [3] and TRANSPATH [4]. Le Bechec et al [5] have created a database (MIR@NT@N) that stores predicted interactions between: a) a TF and its target genes (including microRNAs) and b) microRNAs and their predicted target genes.…”