Sat, 05 Jul 2008 12:22:01 BST CiteULike: emptyhb's modeling_gene_network http://www.citeulike.org/user/emptyhb/tag/modeling_gene_network CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/emptyhb/article/2607945 <i>Nature Methods, Vol. 5, No. 4., pp. 297-298.</i> Levers and fulcrums: progress in cis-regulatory motif models Ewan Birney doi:10.1038/nmeth0408-297 Nature Methods, Vol. 5, No. 4., pp. 297-298. 2008-03-28T16:35:47-00:00 Nature Methods 1548-7091 5 4 297 298 Nature Publishing Group cis_regulatory_elements modeling_gene_network http://www.citeulike.org/user/emptyhb/article/2743944 <i>PLoS genetics, Vol. 4, No. 3. (March 2008)</i><br /><br />Transcription factors (TFs) regulate gene expression through specific interactions with short promoter elements. The same regulatory protein may recognize a variety of related sequences. Moreover, once they are detected it is hard to predict whether highly similar sequence motifs will be recognized by the same TF and regulate similar gene expression patterns, or serve as binding sites for distinct regulatory factors. We developed computational measures to assess the functional implications of variations on regulatory motifs and to compare the functions of related sites. We have developed computational means for estimating the functional outcome of substituting a single position within a binding site and applied them to a collection of putative regulatory motifs. We predict the effects of nucleotide variations within motifs on gene expression patterns. In cases where such predictions could be compared to suitable published experimental evidence, we found very good agreement. We further accumulated statistics from multiple substitutions across various binding sites in an attempt to deduce general properties that characterize nucleotide substitutions that are more likely to alter expression. We found that substitutions involving Adenine are more likely to retain the expression pattern and that substitutions involving Guanine are more likely to alter expression compared to the rest of the substitutions. Our results should facilitate the prediction of the expression outcomes of binding site variations. One typical important implication is expected to be the ability to predict the phenotypic effect of variation in regulatory motifs in promoters. Functional characterization of variations on regulatory motifs. L Michal O Mizrahi-Man Y Pilpel doi:10.1371/journal.pgen.1000018 PLoS genetics, Vol. 4, No. 3. (March 2008) 2008-05-02T03:05:39-00:00 2008 PLoS genetics 1553-7404 4 3 modeling_gene_network transcriptional_regulation http://www.citeulike.org/user/emptyhb/article/2193326 <i>Nature (02 January 2008)</i> Predicting expression patterns from regulatory sequence in Drosophila segmentation Eran Segal Tali Raveh-Sadka Mark Schroeder Ulrich Unnerstall Ulrike Gaul doi:10.1038/nature06496 Nature (02 January 2008) 2008-01-04T06:05:33-00:00 2008 Nature 0028-0836 Nature Publishing Group cis_regulatory_elements drosophila modeling_gene_network http://www.citeulike.org/user/emptyhb/article/874325 <i>Nat Genet (17 September 2006)</i><br /><br />Here we present a quantitative and predictive model of the transcriptional readout of the proximal 1.7 kb of the control region of the Drosophila melanogaster gene even skipped (eve). The model is based on the positions and sequence of individual binding sites on the DNA and quantitative, time-resolved expression data at cellular resolution. These data demonstrated new expression features, first reported here. The model correctly predicts the expression patterns of mutations in trans, as well as point mutations, insertions and deletions in cis. It also shows that the nonclassical expression of stripe 7 driven by this fragment is activated by the protein Caudal (Cad), and repressed by the proteins Tailless (Tll) and Giant (Gt). Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Hilde Janssens Shuling Hou Johannes Jaeger Ah-Ram Kim Ekaterina Myasnikova David Sharp John Reinitz doi:10.1038/ng1886 Nat Genet (17 September 2006) 2006-09-26T20:33:36-00:00 2006 Nat Genet 1061-4036 cis_regulatory_elements drosophila even-skipped_enhancer modeling_gene_network http://www.citeulike.org/user/emptyhb/article/2175731 <i>Cell, Vol. 131, No. 7. (28 December 2007), pp. 1354-1365.</i><br /><br />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. A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell Richard Bonneau Marc Facciotti David Reiss Amy Schmid Min Pan Amardeep Kaur Vesteinn Thorsson Paul Shannon Michael Johnson Christopher Bare William Longabaugh Madhavi Vuthoori Kenia Whitehead Aviv Madar Lena Suzuki Tetsuya Mori Dong-Eun Chang Jocelyne Diruggiero Carl Johnson Leroy Hood Nitin Baliga doi:10.1016/j.cell.2007.10.053 Cell, Vol. 131, No. 7. (28 December 2007), pp. 1354-1365. 2007-12-27T20:18:55-00:00 2007 Cell 131 7 1354 1365 modeling_gene_network