Microarray and RNA-seq experiments have become an important part of modern genomics and systems biology. Obtaining meaningful biological data from these experiments is an arduous task that demands close attention to many details. Negligence at any step can lead to gene expression data containing inadequate or composite information that is recalcitrant for pattern extraction. Therefore, it is imperative to carefully consider experimental design before launching a time-consuming and costly experiment.
Contemporarily, most genomics experiments have two objectives:
- generate two or more groups of comparable data for identifying differentially expressed genes, gene families, biological processes, or metabolic pathways under experimental condition.
- build local gene regulatory networks and identify hierarchically important regulators governing biological processes and pathways of interest.
Since the first objective aims to identify the active molecular identities and the second provides a basis for understanding the underlying molecular mechanisms through inferring causality relationships mediated by treatment, an optimal experiment is to produce biologically relevant and extractable data to meet both objectives without substantially increasing the cost. This review discussed the major issues that researchers commonly face when embarking on a microarray or RNA-seq experiments and summarized important aspects of experimental design, which aim to help researchers deliberate how to generate gene expression profiles with low background noise but more interaction to facilitate novel biological knowledge discoveries in modern plant genomics.