Biologists using modern experimental methods are generating massive amounts of genome-scale data, capturing molecular-level changes in diverse cellular conditions. These large data collections are noisy, highly heterogeneous and must be interpreted in the context of tissue- and cell-type specificity — key aspects to understanding the precise actions of genes and their role in human disease. Integrative methods can prioritize relevant experiments and distill entire functional genomics data collections into gene interaction networks. However, proper visualization of these system-level summaries is critical to gleaning biological insights, particularly when studying gene functions across diverse tissues and cell types. In this talk, we will discuss current approaches and challenges in visualizing and interrogating large-scale functional genomics data. I will introduce our work on visualizing genome-scale tissue- specific functional networks (http://hb.flatironinstitute.org) and describe how biomedical researchers can leverage these tools to interpret the functions of candidate disease genes.