BACKGROUND: Chronic renal diseases are currently classified based on morphological similarities such as whether they produce predominantly inflammatory or non-inflammatory responses. However, such classifications do not reliably predict the course of the disease and its response to therapy. In contrast, recent studies in diseases such as breast cancer suggest that a classification which includes molecular information could lead to more accurate diagnoses and prediction of treatment response. This article describes how we extracted gene expression profiles from biopsies of patients with chronic renal diseases, and used network visualizations and associated quantitative measures to rapidly analyze similarities and differences between the diseases. RESULTS: The analysis revealed three main regularities: (1) Many genes associated with a single disease, and fewer genes associated with many diseases. (2) Unexpected combinations of renal diseases that share relatively large numbers of genes. (3) Uniform concordance in the regulation of all genes in the network. CONCLUSION: The overall results suggest the need to define a molecular-based classification of renal diseases, in addition to hypotheses for the unexpected patterns of shared genes and the uniformity in gene concordance. Furthermore, the results demonstrate the utility of network analyses to rapidly understand complex relationships between diseases and regulated genes.

Real life data can often be modeled as graphs, in which nodes represent objects and edges between nodes indicate their relationships. Large graph datasets are common in many emerging applications. Examples span from social networks, biological networks to computer networks. To fully exploit the wealth of information encoded in graphs, systems for managing and analyzing graph data are critical. To address this need, we have designed and developed a graph querying toolkit, called Periscope/GQ. This toolkit is built on top of a traditional RDBMS. It provides a uniform schema for storing graphs in the database and supports various graph query operations, especially sophisticated operations, such as approximate graph matching, large graph alignment and graph summarization. Users can easily combine several operations to perform complex analysis on graphs. In addition, Periscope/GQ employs several novel indexing techniques to speed up query execution. This demonstration will highlight the use of Periscope/GQ in two application domains: life science and social networking.