Thu, 21 Aug 2008 15:16:20 BST CiteULike: eldan yeast http://www.citeulike.org/user/eldan/tag/yeast CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/eldan/article/1190676 <i>Biosystems, Vol. 88, No. 1-2. (March 2007), pp. 163-172.</i><br /><br />Alternative pathways through a gene regulation network connect a regulatory molecule to its (indirect) regulatory target via different intermediate regulators. We here show for two large transcriptional regulation networks, and for 15 different signal transduction networks, that multiple alternative pathways between regulator and target pairs are the rule rather than the exception. We find that in the yeast transcriptional regulation network intermediate regulators that are part of many alternative pathways between a regulator and target pair evolve at faster rates. This variation is not solely explicable by higher expression levels of such regulators, nor is it solely explicable by their variable usage in different physiological or environmental conditions, as indicated by their variable expression. This suggests that such pathways can continue to function despite amino acid changes that may impair one intermediate regulator. Our results underscore the importance of systems biology approaches to understand functional and evolutionary constraints on genes and proteins. Alternative routes and mutational robustness in complex regulatory networks Andreas Wagner Jeremiah Wright doi:10.1016/j.biosystems.2006.06.002 Biosystems, Vol. 88, No. 1-2. (March 2007), pp. 163-172. 2007-03-28T02:59:45-00:00 2007 Biosystems 88 1-2 163 172 genetic_regulatory_networks yeast http://www.citeulike.org/user/eldan/article/1065778 <i>Science, Vol. 298, No. 5594. (October 2002), pp. 799-804.</i><br /><br />We have determined how most of the transcriptional regulators encoded in the eukaryote Saccharomyces cerevisiae associate with genes across the genome in living cells. Just as maps of metabolic networks describe the potential pathways that may be used by a cell to accomplish metabolic processes, this network of regulator-gene interactions describes potential pathways yeast cells can use to regulate global gene expression programs. We use this information to identify network motifs, the simplest units of network architecture, and demonstrate that an automated process can use motifs to assemble a transcriptional regulatory network structure. Our results reveal that eukaryotic cellular functions are highly connected through networks of transcriptional regulators that regulate other transcriptional regulators. Transcriptional Regulatory Networks in Saccharomyces cerevisiae Tong Lee Nicola Rinaldi François Robert Duncan Odom Ziv Bar-Joseph Georg Gerber Nancy Hannett Christopher Harbison Craig Thompson Itamar Simon Julia Zeitlinger Ezra Jennings Heather Murray Benjamin Gordon Bing Ren John Wyrick Jean-Bosco Tagne Thomas Volkert Ernest Fraenkel David Gifford Richard Young doi:10.1126/science.1075090 Science, Vol. 298, No. 5594. (October 2002), pp. 799-804. 2007-01-25T02:38:36-00:00 2002 Science 298 5594 799 804 genetic_regulatory_networks yeast http://www.citeulike.org/user/eldan/article/1048296 <i>PNAS, Vol. 101, No. 14. (6 April 2004), pp. 4781-4786.</i><br /><br />The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle regulatory network of the budding yeast. With the use of a simple dynamical model, it was demonstrated that the cell-cycle network is extremely stable and robust for its function. The biological stationary state, the G1 state, is a global attractor of the dynamics. The biological pathway, the cell-cycle sequence of protein states, is a globally attracting trajectory of the dynamics. These properties are largely preserved with respect to small perturbations to the network. These results suggest that cellular regulatory networks are robustly designed for their functions. 10.1073/pnas.0305937101 The yeast cell-cycle network is robustly designed Fangting Li Tao Long Ying Lu Qi Ouyang Chao Tang doi:10.1073/pnas.0305937101 PNAS, Vol. 101, No. 14. (6 April 2004), pp. 4781-4786. 2007-01-17T23:27:11-00:00 2004 PNAS 101 14 4781 4786 boolean_networks genetic_regulatory_networks yeast