A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell

@article{bfr-pmtcp-2007, abstract = {Summary The environment significantly influences the dynamic expression and assembly of all components encoded in the genome of an organism into functional biological networks. We have constructed a model for this process in Halobacterium salinarum NRC-1 through the data-driven discovery of regulatory and functional interrelationships among ~80\% of its genes and key abiotic factors in its hypersaline environment. Using relative changes in 72 transcription factors and 9 environmental factors (EFs) this model accurately predicts dynamic transcriptional responses of all these genes in 147 newly collected experiments representing completely novel genetic backgrounds and environments--suggesting a remarkable degree of network completeness. Using this model we have constructed and tested hypotheses critical to this organism's interaction with its changing hypersaline environment. This study supports the claim that the high degree of connectivity within biological and EF networks will enable the construction of similar models for any organism from relatively modest numbers of experiments.}, author = {Bonneau, Richard and Facciotti, Marc T. and Reiss, David J. and Schmid, Amy K. and Pan, Min and Kaur, Amardeep and Thorsson, Vesteinn and Shannon, Paul and Johnson, Michael H. and Bare, Christopher J. and Longabaugh, William and Vuthoori, Madhavi and Whitehead, Kenia and Madar, Aviv and Suzuki, Lena and Mori, Tetsuya and Chang, Dong-Eun and Diruggiero, Jocelyne and Johnson, Carl H. and Hood, Leroy and Baliga, Nitin S. }, citeulike-article-id = {2175731}, doi = {10.1016/j.cell.2007.10.053}, journal = {Cell}, keywords = {actex, network\_modules}, month = {December}, number = {7}, pages = {1354--1365}, posted-at = {2007-12-29 15:26:16}, priority = {5}, title = {A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell}, url = {http://dx.doi.org/10.1016/j.cell.2007.10.053}, volume = {131}, year = {2007} }

TY - JOUR ID - bfr-pmtcp-2007 L3 - citeulike-article-id:2175731 TI - A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell JF - Cell VL - 131 IS - 7 SP - 1354 EP - 1365 N2 - Summary The environment significantly influences the dynamic expression and assembly of all components encoded in the genome of an organism into functional biological networks. We have constructed a model for this process in Halobacterium salinarum NRC-1 through the data-driven discovery of regulatory and functional interrelationships among ~80% of its genes and key abiotic factors in its hypersaline environment. Using relative changes in 72 transcription factors and 9 environmental factors (EFs) this model accurately predicts dynamic transcriptional responses of all these genes in 147 newly collected experiments representing completely novel genetic backgrounds and environments--suggesting a remarkable degree of network completeness. Using this model we have constructed and tested hypotheses critical to this organism's interaction with its changing hypersaline environment. This study supports the claim that the high degree of connectivity within biological and EF networks will enable the construction of similar models for any organism from relatively modest numbers of experiments. KW - actex KW - network_modules AU - Bonneau, Richard AU - Facciotti, Marc AU - Reiss, David AU - Schmid, Amy AU - Pan, Min AU - Kaur, Amardeep AU - Thorsson, Vesteinn AU - Shannon, Paul AU - Johnson, Michael AU - Bare, Christopher AU - Longabaugh, William AU - Vuthoori, Madhavi AU - Whitehead, Kenia AU - Madar, Aviv AU - Suzuki, Lena AU - Mori, Tetsuya AU - Chang, Dong-Eun AU - Diruggiero, Jocelyne AU - Johnson, Carl AU - Hood, Leroy AU - Baliga, Nitin PY - 2007/12/28/ UR - http://dx.doi.org/10.1016/j.cell.2007.10.053 ER -