Reading the Palimpsest of Cell Interactions: What Questions May We Ask of the Data?

Biological function depends on the composition as well as structure of the organism, that is the organization of interactions between its parts. In multicellular organisms, the complex communication between cells is crucial for the coordination of cellular functions (growth, differentiation, apoptosis), compartmentalization of cellular processes within the organism, and the integration of cells into functioning higher levels of structural organization. Here we focus on the interaction among cells, as the basic level of biological organization, capable of a remarkable degree of autonomy and self-maintenance. While a wealth of data on putative cell interactions has recently become available, its biological interpretation depends on expectations we have for the structure of these interaction networks. This contribution is an attempt at formulating basic questions we may ask about cell interaction data. We build on the understanding that cells fulfill two general functions: the integrity-maintaining and the organismal service function. We derive the expected patterns of cell interactions considering two intertwined aspects: the immediate functional and the evolutionary. Based on these, we propose several guidelines for analysis and interpretation of transcriptional cell-interactome data.