Prediction of gene function and regulation

General info

Date from - to

01 Nov 2005 - 01 Jan 2010

Project leader(s)

ter Braak, Cajo Prof. Dr.

Participant(s)

Ham, van Roeland Dr.

Cuppen, Edwin Prof. dr.

Abstract

To predict the function and regulation of genes, evidence from various data sources has to be pieced together. The challenge is to do this on a genome-wide scale and with significant sensitivity and specificity. This project distinguishes three research lines:

• A probabilistic framework for gene function prediction, based on Saccharomyces cerevisiae. This framework is being expanded to more complex plant genomes.
• The role of alternative splicing in gene functionalisation in plants, as well as its impact on computational methods of gene function prediction.
• Genomes of animal species are explored for functional elements and genetic variations, concentrating on non-protein coding genomic elements (e.g. promoter elements, but also microRNA-coding sequences).

Link to the end report of this project

Publications

• SNP and haplotype mapping for genetic analysis in the rat
• Distribution and functional impact of DNA copy number variation in the rat
• Limitations and possibilities of small RNA digital gene expression profiling
• Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome
• A genome-wide SNP panel for mapping and association studies in the rat