To investigate the structure of the genomic interaction network built from yeast gene-expression compendium dataset of hundreds of systematic perturbations, social affiliation network analysis methodologies were applied through quantifying various density, closeness and centrality measures and exploring core-periphery structures. Genes affected by a larger number of perturbations were found to be involved in responses to various environmental challenges. Deletion of essential genes was suggested to cause larger number of genes to be significantly up or down regulated. We explored the network structure made up of several sub-networks using core-periphery models to find ancient pathways. Glycolysis and TCA cycle have relatively core positions in the energy-related processes of yeast.
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