Lessons from Cellular Networks

Hanah Margalit, The Hebrew University of Jerusalem

The genome projects and following high-throughput experiments generate large amounts of data of various types, such as the arrangement of genes on the chromosome, and their expression and regulation patterns. A major challenge is to analyze this large body of data and infer new biological knowledge. Representing the various types of data as networks of molecular relations opens new ways for exploring the mechanistic modules and the underlying evolutionary forces that shape the cellular circuitry. Interesting insights can be gained by comparing the networks of various organisms and by integrating networks that contain different types of connections. I will present our work on integrative analysis of networks and especially focus on the association between transcription regulation and the order of genes on the chromosome. By representing chromosomal adjacency of genes as a network and integrating it with the transcriptional regulatory network we revealed links between transcription regulation and chromosomal organization in both E. coli and Saccharomyces cerevisiae. Two major phenomena were found: common regulation of neighbors (in both organisms) and neighbor regulation (only in E. coli). Our findings suggest that in both organisms transcription regulation has shaped the organization of transcription units on the chromosome. Differences found between the organisms reflect the inherent differences in transcription regulation between pro- and eukaryotes.