Gene regulation at the level of transcription is crucial for almost all biological processes in a cell or organism. Transcription factors are sequence-specific DNA-binding proteins that are capable of activating and/or repressing transcription. Therefore, studying transcription factors helps in better understanding biological processes. One such family is the large MADS domain family and its members in plants have been shown to be involved in, e.g. flowering, root, flower, and fruit development. Mutations in genes of this family can cause homeotic changes. However, a large part of this family is still not characterized and how its members function at the molecular level is still not clear. This book presents the results obtained in the characterization of the complete Arabidopsis MADS domain family. Different perspectives were taken to obtain a global overview of this important transcription factor family at the gene and protein level and it opens new avenues to a more Systems Biology way of understanding. This book should be especially useful to students and scientists interested in MADS domain proteins, but also to whom is interested in genomics analyses in general.