Within a cell, such as the neuron shown here, genetic differences as well as differences in gene expression (mRNA), protein expression, and small molecule expression (such as neurotransmitters) characterize the epileptic focus. These individual molecular systems must also be placed within the contexts of larger systems including organ, tissue, and cell type. The complexity of this system creates one of the greatest challenges for the study and interpretation of high-throughput molecular profiling methods in epilepsy.