Supplementary Information

Similarities and differences of gene expression in
yeast stress conditions

Oleg Rokhlenko ^a, Ydo Wexler ^a and Zohar Yakhini ^a,b

^aTechnion-Israel Institute of Technology, Computer Science Dept. Haifa, 32000, Israel
^bAgilent Laboratories, Palo Alto, CA

Abstract

 Motivation and Methods:

All living organisms and the survival of all cells critically depend on their ability to sense and quickly adapt to changes in the environment and to other stress conditions. We study stress response mechanisms in Saccharomyces cerevisiae by identifying genes that, according to very stringent criteria, have persistent co-expression under a variety of stress conditions. This is enabled through a fast clique search method applied to the intersection of several co-expression graphs calculated over the data of Gasch et al. [3]. This method exploits the topological characteristics of these graphs.
 

Results:

We observe cliques in the intersection graphs that are much larger than expected under a null model of changing
gene identities for different stress conditions but maintaining the co-expression topology within each one. Persistent cliques are analyzed to identify enriched function as well as enriched regulation by a small number of TFs. These TFs
therefore characterize a universal and persistent reaction to stress response. We further demonstrate that the vertices
(genes) of many cliques in the intersection graphs are colocalized in the yeast genome, to a degree far beyond the
random expectation. Co-localization can hypothetically contribute to a quick co-ordinated response. We propose the
use of persistent cliques in further study of properties of co-regulation.

Supplementary Data