Genome-scale analysis of interaction dynamics reveals organization of biological networks by Jishnu Das, Jaaved Mohammed, and Haiyuan Yu. (Bioinformatics (2012) 28 (14): 1873-1878. doi: 10.1093/bioinformatics/bts283)
Analyzing large-scale interaction networks has generated numerous insights in systems biology. However, such studies have primarily been focused on highly co-expressed, stable interactions. Most transient interactions that carry out equally important functions, especially in signal transduction pathways, are yet to be elucidated and are often wrongly discarded as false positives. Here, we revisit a previously described Smith–Waterman-like dynamic programming algorithm and use it to distinguish stable and transient interactions on a genomic scale in human and yeast. We find that in biological networks, transient interactions are key links topologically connecting tightly regulated functional modules formed by stable interactions and are essential to maintaining the integrity of cellular networks. We also perform a systematic analysis of interaction dynamics across different technologies and find that high-throughput yeast two-hybrid is the only available technology for detecting transient interactions on a large scale.
Research of obvious importance to anyone investigating biological networks but I mention it for the problem of how to represent transient relationships/interactions in a network?
Assuming a graph/network typology, how does a transient relationship impact a path traversal?
Assuming a graph/network typology, do we ignore the transience for graph theoretical properties such as shortest path?
Do we need graph theoretical queries versus biological network queries? Are the results always the same?
Can transient relationships results in transient properties? How do we record those?
Better yet, how do we ignore transient properties and under what conditions? (Leaving to one side how we would formally/computationally accomplish that ignorance.) What are the theoretical issues?
You can find the full text of this article at Professor Yu’s site: http://yulab.icmb.cornell.edu/PDF/Das_B2012.pdf