Highlighting relationships between heterogeneous biological data through graphical displays based on regularized canonical correlation analysis

Biological data produced by high throughput technologies are becoming more and more abundant and are arousing many statistical questions. This paper addresses one of them; when gene expression data are jointly observed with other variables with the purpose of highlighting significant relationships between gene expression and these other variables. One relevant statistical method to explore these relationships is Canonical Correlation Analysis (CCA). Unfortunately, in the context of postgenomic data, the number of variables (gene expressions) is usually greater than the number of units (samples) and CCA cannot be directly performed: a regularized version is required. We applied regularized CCA on data sets from two different studies and show that its interpretation evidences both previously validated relationships and new hypothesis. From the first data sets (nutrigenomic study), we generated interesting hypothesis on the transcription factor pathways potentially linking hepatic fatty acids and gene expression. From the second data sets (pharmacogenomic study on the NCI-60 cancer cell line panel), we identified new ABC transporter candidate substrates which relevancy is illustrated by the concomitant identification of several known substrates. In conclusion, the use of regularized CCA is likely to be relevant to a number and a variety of biological experiments involving the generation of high throughput data. We demonstrated here its ability to enhance the range of relevant conclusions that can be drawn from these relatively expensive experiments.