Dissecting complex transcriptional responses using pathway-level scores based on prior information

Background: The genomewide pattern of changes in mRNA expression measured using DNA microarrays is typically a complex superposition of the response of multiple regulatory pathways to changes in the environment of the cells. The use of prior information, either about the function of the protein encoded by each gene, or about the physical interactions between regulatory factors and the sequences controlling its expression, has emerged as a powerful approach for dissecting complex transcriptional responses. Results: We review two different approaches for combining the noisy expression levels of multiple individual genes into robust pathway-level differential expression scores. The first is based on a comparison between the distribution of expression levels of genes within a predefined gene set and those of all other genes in the genome. The second starts from an estimate of the strength of genomewide regulatory network connectivities based on sequence information or direct measurements ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Harmen J. Bussemaker, Lucas D. Ward, André Boorsma
• Keywords: BMCBI 2007, Expression Levels, Multiple Regulatory Pathways, Regulatory Pathways