BACKGROUND AND SCOPE OF THE PROGRAMME

It is estimated that around 40% of the open reading frames in a fully sequenced organism have no known function at the biochemical level and are unrelated to any known gene, while at the level of phenotype the proportion with known properties is much less. Consequently, a shift of emphasis is now occurring from genome mapping and sequencing to determination of genome function. This is the area known as functional genomics, which has been described as 'the development and application of global (genome-wide or system-wide) experimental approaches to assess gene function by making use of the information and reagents provided by genome sequencing and mapping' (Hietor,P. and Boguski,M. (1997) Science 278:601). Functional genomics has emerged recently as a new discipline employing major innovative technologies for genome-wide analysis supported by information technology. These activities depend both on experimental and computational methods. While high throughput experimental technologies generate data on gene expression, protein structure, protein interactions, etc., powerful information systems are required for the efficient management of experimental data, integration of information that is distributed in heterogeneous sources and establishment of 'computer assisted experimental strategies'.

Acknowledging the need to integrate experimental technologies with each other and with informatics tools, a structure is required which addresses bottleneck problems. We have identified a set of 'vertical' and 'horizontal' scientific areas that will be used to structure the organisation of our cooperation at the European level. Vertical areas correspond to specific technological or scientific fields, while horizontal areas correspond to requirements that are common to several vertical areas. A vertical organisation is needed to foster collaborations in the development of parallel techniques, such as the individual technologies of expression profiling, proteomics and mutation analysis, in order to facilitate exchange and communication within particular fields. At the same time, a horizontal organisation is required to integrate functional and expression data from different sources with databases and literature information through bioinformatics tools having universal application.

The vertical areas are:
1. Analysis of phenotypic changes resulting from mutagenesis and gene disruption.
2. DNA arrays and chips in expression profiling and mutation detection.
3. Proteomics: protein identification, characterisation, expression and interactions.
4. Structural genomics: protein structure determination, classification, modelling and docking.
5. In silico methods for the description of cellular systems by data and literature mining, predictions and simulations.

The horizontal areas are:
1. Standardisation, benchmarking and comparison of different experimental systems.
2. Data management: databases, interfaces and ontologies.
3. Combination and integration of functional genomics data to derive new biological knowledge.

The activities of this programme will encourage linkages between groups with expertise in different experimental and informational aspects of functional genomics through workshops, training courses, short term inter-laboratory visits and this web site which will integrate functional genomics in an interdisciplinary manner.