CRP-DNA Complex
PRODORIC logo Release 8.9
up About the Project

The PRODORIC project was initiated in the course of the foundation of the Bioinformatics Competence Center Braunschweig "Intergenomics" in 2001. It is one of six competence centers in Germany. The goal of the research and development of this competence center is to provide a range of bioinformatics tools that are suitable to model the interaction of genome-driven processes during the microbial infection of mammalian and plant organisms.

The project is funded by the German Bundesministerium für Bildung und Forschung (BMBF) and is managed by the Project Management Organisation Jülich (PTJ) and National Genome Research Network (NGFN).

The microbial part of the project (PRODORIC) is maintained at the Technical University of Braunschweig in the Institute of Microbiology.

tubs logo nbcc logo bmbf nfgn

PRODORIC is an acronym for PROcariotIC Database Of Gene-Regulation (the term "doric" refers to greek columns, that's why there is a the greek temple on the home page). This database is an integrated approach to provide information about molecular networks in prokaryotes with focus on pathogenic organisms. In detail this concerns:

  • transcriptional regulation (transcription factors and their DNA binding sites
  • signal transduction (two-component systems, phosphylation cascades)
  • protein interactions (complex formation, oligomerization)
  • biochemical pathways (chemical reactions)
  • other regulation events (e.g. codon usage, etc. ...)
In the long term it aims to be a resource to model protein-host interactions. Furthermore it will be a suitable platform to analyze high-throughput data from proteomis and transcriptomics experiments (systems biology).

Currently PRODORIC mainly contains detailed information about operon and promoter structures including huge collections of transcription factor binding sites. If an appropriate number of regulatory binding sites is available, a position weight matrix (PWM) and a sequence logo is provided, which can be used to predict new binding sites (see tools). This data is collected manually by screening the original scientific literature.

More recently PRODORIC was extended to handle protein-protein interactions and signal-transduction cascades that commonly occur in form of two-component systems in prokaryotes. Furthermore PRODORIC contains metabolic network data imported from the KEGG database.

A number of database associated tools were developed for the prediction and visualization of data. For more details concerning our tools please visit the Tools Section of our website.


up Annotation and Content

All entries of PRODORIC are generated de novo by manually input with exception of the core data. This is done by constantly screening the scientific literature for relevant data. Therefore, the data collection is unique as it does not rely on other compilations or in silico predictions.PRODORIC stores the core data for nearly every sequenced bacterialgenome.

Nevertheless, there exist only annotated data for a subset of organisms. On one hand research often focuses on selected model organisms. On the other hand the annotation process lags behind the ongoing flood of experimental data.

Besides the organization of the core data the main amount of data concentrates on TFBSs and associated data. TFBSs are directly linked to its respective genome, promoter and regulated genes. They are organized in profiles and used to construct PWMs. Currently, more than 2500 TFBSs directly extracted from the scientific literature are stored in PRODORIC which is probably the largest collection in this field. Based on these data a huge library of about 170 profiles and PWMs is provided. In many cases species-specific PWMs of the respective regulators are available that allow a more specific prediction of potentially new TFBSs.

Since release 2 published expression data are also integrated. This mainly comprises induction levels of genes under various environmental conditions or in certain mutant strains. These data are directly linked to genes of PRODORIC. There are currently 120 expression profiles stored comprising links to about 9000 genes. A detailed statistics is available here.


up Database Structure

Since PRODORIC is a genome based database it contains the whole bacterial genome sequences including the annotated ORFs and protein sequences. For this purpose the respective data available at the NCBI server and the genome reviews present at the EBI was imported into PRODORIC. Additionally the compounds and reactions of the KEGG database were integrated. These fundamental data are referred to as core data as they describe the major cellular components (genes, proteins and biochemical molecules) which are usually in the focus of annotation.

These core data were organized into a relational structure to allow the modeling of various biological features and molecular interactions as accurate as possible. These included special microbial features like operon and typical prokaryotic promoter structures as well as higher order protein complexes. Therefore, the concept of protein states was implemented since the direct gene product (here referred to as polypeptide) is often organized in protein complexes and/or differentially modified. The database was designed to allow various interaction types within the core data. These include amongst others interactions between different proteins, proteins with DNA binding sites or environmental growth conditions with the corresponding expression profiles. Hereby a central linking table was introduced for a modular extensibility of new interaction or reaction types.

In this figure the central part of the database is shown schematically as UML model.

prodoric_uml

up Web Interface & Technology

The web sites require a HTML 4.0-compliant browser (e.g. Mozilla/Firefox, Netscape Navigator, Opera, Chrome or Internet Explorer) with following options: graphics display, JavaScript, Cascaded Style Sheets.

The Display is optimized for a 1024x768 screen resolution. To report problems, broken links or comment on the web site, please write to the email address given in the contact section.

PRODORIC was developed by exclusively using Open Source products and other freely available software.
It runs very stable on a LAPP system (Linux, Apache, PostgreSQL, PHP).
A compilation of all products used to create PRODORIC is shown in the acknowlegdement below. We would like to thank all developers.

tux ubuntu> Linux (SuSE professional distribution)
apache Apache2 web server
postgresql PostgreSQL relational database management system
php PHP hypertext preprocessor for dynamic web pages
phppgadmin Web-based administration tool for PostgreSQL
dbvisualizer Tool to visualize database structures
gcc GNU C++ Compiler
kdevelop KDevelop - KDE development environment
bluefish Web development studio
Quanta Web development tool
ginp GNU Image Manipulation Program
firefox Web browser
buttongenerator Button generator