Bi-directional gene set enrichment and canonical correlation analysis identify key diet-sensitive pathways and biomarkers of met

Background: Currently, a number of bioinformatics methods are available to generate appropriate lists of genes from a microarray experiment. While these lists represent an accurate primary analysis of the data, fewer options exist to contextualise those lists. The development and validation of such methods is crucial to the wider application of microarray technology in the clinical setting. Two key challenges in clinical bioinformatics involve appropriate statistical modelling of dynamic transcriptomic changes, and extraction of clinically relevant meaning from very large datasets. Results: Here, we apply an approach to gene set enrichment analysis that allows for detection of bi-directional enrichment within a gene set. Furthermore, we apply canonical correlation analysis and Fisher's exact test, using plasma marker data with known clinical relevance to aid identification of the most important gene and pathway changes in our transcriptomic dataset. After a 28-day dietary interve...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Melissa J. Morine, Jolene McMonagle, Sinead Toomey, Clare M. Reynolds, Aidan P. Moloney, Isobel Claire Gormley, Peadar Ó Gaora, Helen M. Roche
• Keywords: BMCBI 2010, Canonical Correlation, Plasma Marker Data, Plasma Markers