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Title: A Graph-based Pathway Searching System over a Signal Transduction Database
P102
May, Gerhard H.W.; Gilbert, David

g.may@bio.gla.ac.uk, drg@brc.dcs.gla.ac.uk
Institute of Biomedical and Life Sciences, Davidson Building and Bioinformatics Research Centre, Department of Computing Science, Glasgow

One of the main challenges in the post-genomic era is the development of tools and systems for the storage and analysis of the large amount of data being generated by micro-array and proteomics experiments. One of many aspects of this challenge is the appropriate representation of biochemical networks like metabolic, regulatory, or signal transduction pathways in an appropriate way to allow meaningful queries of the underlying data, for example in searches for pathways through the network.
Several databases exist which provide facilities for storing and searching signalling pathways, amongst them CSNdb1, TRANSPATH2, BIND3, and aMAZE4.
We have designed and implemented a database schema which allows the storage of information regarding signalling complexes and the individual components they consist of, information about any post-translational modification of these components and their state of activity, information about the cellular locations of signalling complexes, and information about signal transduction processes between these signalling molecules. These processes represent mechanisms involved in passing signals/information from molecule to molecule and are modelled as connections between the signalling complexes. Additionally, the database schema allows storage of information about the experimental evidence for any biological process modelled in the database. Links to information in external databases will be incorporated in the information about individual components. The database schema has been implemented in MySQL and is currently being populated with known signalling molecules.
Signalling molecules and connecting processes have been modelled in such a way that they can be treated as vertices and arcs in a signal transduction pathway graph. Each participating complex is considered to be an individual vertex. To facilitate pathway searches over this graph we have implemented a Java-based computational tool. This tool will be available over the web from http://www.brc.dcs.gla.ac.uk in the form of a servlet which creates a simple user interface which in turn allows users to conduct specific pathway searches in the underlying database. Available queries include searches for complexes which are direct neighbours, upstream or downstream, of a given signalling molecule, searches for any pathway or pathways of predetermined length including a given signalling molecule, searches for possible pathways connecting two (or more) molecules of choice, and searches for circular pathways which could represent feedback inhibitory or stimulatory loops in the underlying regulatory network.
This database and query tool is forming the first module of a planned integrated suite of tools designed to help lab-based researchers in planning experiments and analysing resulting data.
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[3] Bader, G.D., Donaldson, I., Wolting, C., Ouellette, B.F.F., Pawson, T. & Hogue, C.W.V. (2001) BIND - The Biomolecular Interaction Network Database. Nucl Acids Res 29, 242-245.
[4] van Helden, J., Naim, A., Manusco, R., Eldridge, M., Wernisch, L., Gilbert, D. & Wodak, S.J. (2000) Representing and analysing molecular and cellular function using the computer. Biol Chem 381, 921-935.