Crossing borders between biology and data analysis

Important factors in a top down systems biology study.

In top down systems biology, the answer to a certain biological question is sought in
the systems wide response of a biological system to the chosen experimental conditions. The response of the biological system is measured with -omics tools, such as, transcriptomics or metabolomics, and advanced data analysis tools are applied to extract biologically relevant information from the measurements. The success of a top down systems biology approach is highly dependent on the information richness of the data obtained from the -omics measurements. Therefore, it is essential for a successful top down systems biology study to balance the three key factors: (i) biological question, (ii) experimental design, and (iii) data analysis. In Chapter 1, we discuss these three key factors, their interdependence, and their significance for successful top down systems biology. In Chapters 2 to 6, different aspects of the relation between a biological question and a data analysis strategy, such as, data pretreatment and selection of the most suited data analysis method, are further explored.