Institute of Bioinformatics
Center of Informatics,Statistics and Epidemiology UMG, University of Göttingen
On these pages we provide links to databases and analysis tools resulting from our own research and development projects. In addition, a number of important external tools which fit to our research focus are mirrored. Furthermore we're providing our own Linux-on-a-disk-solution named Göbix (based on Knoppix).Please note that some of the services are offered exclusively to members of Göttingen University.
CYTOMER is a relational database on organs/tissues, cell types, physiological systems and developmental stages, presently focussing on the human system. From this database, an ontology for anatomical, morphological structures for the human organism, including all embryonal stages, and the cell types constituting these structures is derived.
DiVa (Disconnectivity Valuation tool) is a program running in a console that counts the pairwise disconnectivity index of individual elements in large regulatory networks. Such an element might be a vertex (i.e., molecules, genes), an edge (i.e., reactions, interactions), as well as a group of vertices and/or edges. The index evaluates the capacity of an element to disconnect reachable pairs of vertices upon its removal from the network. The index quantifies how critical an individual element is for sustaining the pairwise regulatory communication within the whole network.
EndoNet is a new database about the components of endocrine networks and their relations. It focuses on the endocrine cell-to-cell signaling and visualizes human intercellular regulatory pathways.
For further details of the EndoNet project, see.
GöBIX is a Live-DVD based on Knoppix and extended with several tools useful for bioinformatics. You can boot from this CD/DVD and use all the tools, while your installed operating system isn't changed at all. It is very suitable to repeat and prepare the Linux-Perl course.
Because GöBIX is mainly an additional help for students in Göttingen visiting our courses, the description is in german only. Inside GöBIX the default language is german where available, but can also be changed.
PathoDB® Professional is a database on pathologically relevant mutated forms of transcription factors and their binding sites. It comprises numerous cases of defective transcription factors or mutated transcription factor binding sites, which are known to cause pathological defects. The underlying genetic defects and the resulting diseases are considered as well. PathoDB® is developed by Biobase and only available for members of the UKG.
Please read the license conditions before using PathoDB.
ReAlSplice collects information on the splicing sites which will be "glued" together during the splicing event, on additional sites in the pre-mRNA which are regarded to influence alternative splicing and on factors involved in alternative splicing (i.e. splicing factors).
S/MARt DB collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the whole range from yeast to human.
It covers the whole range from yeast to human. For convenience S/MARt DB provides links to Medline abstracts of the extracted publications, relevant entries in primary sequence databases, (EMBL/GenBank/DDBJ, SwissProt and PIR) and to databases devoted to gene regulation (Transfac and TRRD).
TiProD is a database of human promoter sequences for which some functional features are known. It allows a user to query individual promoters and the expression pattern they mediate, gene expression signatures of individual tissues, and to retrieve sets of promoters according to their tissue-specific activity or according to individual Gene Ontology terms the corresponding genes are assigned to. We have defined a measure for tissue-specificity that allows the user to discriminate between ubiquitously and specifically expressed genes or any Gene Ontology (GO)-assignment, e.g. to a given biological process.
This is a classification of eukaryotic transcription factors (TFs) according to their DNA-binding domains. The present classification focuses on human TFs and its rodent homologs, but will be extended to other eukaryotic taxa in the future. You can find more details here, or go straight to the classification here.
The TRANSFAC® database helps researchers to understand the transcriptional control of genes.Functionally regulated and disregulated conditions are provided in different databases. Each of the databases deals with one special feature in eukaryotic cells.TRANSFAC® delivers any information on transcription factors, their genomic binding sites and the regulated genes.Based on the binding sites matrices which can be retrieved from multiple site entries in the TRANSFAC® database analysis tools can be used to elucidate new potential target genes. TRANSFAC® Professional is developed by Biobase and only available for members of the UKG.
Please read the license conditions before using TRANSFAC® Professional.
TRANSPATH® Professional comprises data about molecules participating in signal transductionand the reactions they undergo, thus spanning a complex network of interconnected signalling components. TRANSPATH® Professional focuses on signalling cascades that aim at transcription factors and thus alter the gene expression profile of a given cell.TRANSPATH® Professional is the resource of choice in disclosing the upstream regulators and downstream targets of each molecule in the regulatory network.
Connected and integrated with the TRANSFAC® Professional database, TRANSPATH® Professional bridges the gap between extra cellular signal molecules (such as hormones, cytokines etc.) and the genes responding to these triggers. TRANSPATH® is developed by Biobase and only available for members of the UKG.
Please read the license conditions before using TRANSPATH®.
TRANSPRO? is a database module within the TRANSFAC® Suite. It contains upstream (5') sequences of human, mouse, and rat genes. The TRANSPRO? sequences can be directly searched for potential regulatory elements with the help of BIOBASE tools such as TRANSPLORER®, Match?, Patch?, and Catch®. TRANSPRO? is developed by Biobase and only available for members of the UKG.
Please read the license conditions before using TRANSPRO?.
TSM, the TRANSFAC Saccharomyces Module is an extensive repository of information on yeast transcription factors and transcription factor binding sites. It is based upon the TRANSFAC database (Matys et al., 2003) and was implemented in the framework of the Comprehensive Yeast Genome Database (CYGD) project.
TRANSCompel® Professional is a specialized database module on composite regulatory elements. Such elements are found in many promoters and enhancers of eukaryotic genes. They consist of two binding sites of two different transcription factors, which through this combination form a module with new regulatory properties. Composite elements frequently serve as integration sites of two (or more) signaling pathways.
TRANSCompel® Professional progresses from single binding events (as in theTRANSFAC® Professional database) to combinatorial regulation, helping to build up structures of entire promoters. TRANSCompel® Professional is developed by Biobase and only available for members of the UKG.
Please read the license conditions before using TRANSCompel® Professional