Dialogue on Reverse-Engineering Assessment and Methods: The DREAM of High-Throughput Pathway Inference

doi:10.1196/annals.1407.021

The biotechnological advances of the last decade have confrontedus with an explosion of genetics, genomics, transcriptomics,proteomics, and metabolomics data. These data need to be organizedand structured before they may provide a coherent biologicalpicture. To accomplish this formidable task, the availabilityof an accurate map of the physical interactions in the cellthat are responsible for cellular behavior and function wouldbe exceedingly helpful, as these data are ultimately the resultof such molecular interactions. However, all we have at thistime is, at best, a fragmentary and only partially correct representationof the interactions between genes, their byproducts, and othercellular entities. If we want to succeed in our quest for understandingthe biological whole as more than the sum of the individualparts, we need to build more comprehensive and cell-context–specificmaps of the biological interaction networks. DREAM, the Dialogueon Reverse Engineering Assessment and Methods, is fosteringa concerted effort by computational and experimental biologiststo understand the limitations and to enhance the strengths ofthe efforts to reverse engineer cellular networks from high-throughputdata. In this chapter we will discuss the salient argumentsof the first DREAM conference. We will highlight both the stateof the art in the field of reverse engineering as well as someof its challenges and opportunities.

Part I. Community Efforts for Pathway Inference

The DREAM of High-Throughput Pathway Inference