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Superimposed on the genetic code as defined by the genome sequence of an eukaryote is a complex layer of chromatin modifications. These reversible covalent modifications of both nucleotide bases such as cytosines and specific residues of various histone tails apparently serve as molecular patterns that can quantitatively affect the output of the genetic code in time and space. With the advent of NextGen sequencing platforms in the past 5 years, ChIP-seq together with RNA-seq are techniques that have revolutionize chromatin related research by enabling high resolution mapping of chromatin modifications as well as transcripts produced in a cell. A major challenge in the field is to extract functionally relevant insights from the large quantity of data generated from these high-throughput technologies. In this talk, we will explore two related data integration and visualization approaches, ANCORP and SSEA, that we have used to reveal correlations between chromatin marks and transcript output in Arabidopsis.