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Amrita Pati Cecilia Vasquez-Robinet Lenwood S Heath Ruth Grene TM Murali 《BMC bioinformatics》2006,7(1):218-14
Background
Modeling of cis-elements or regulatory motifs in promoter (upstream) regions of genes is a challenging computational problem. In this work, set of regulatory motifs simultaneously present in the promoters of a set of genes is modeled as a biclique in a suitably defined bipartite graph. A biologically meaningful co-occurrence of multiple cis-elements in a gene promoter is assessed by the combined analysis of genomic and gene expression data. Greater statistical significance is associated with a set of genes that shares a common set of regulatory motifs, while simultaneously exhibiting highly correlated gene expression under given experimental conditions. 相似文献2.
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Michael Tillich Vinh Le Sy Katrin Schulerowitz Arndt Haeseler von Uwe G Maier Christian Schmitz-Linneweber 《BMC evolutionary biology》2009,9(1):201
Background
RNA editing in chloroplasts of angiosperms proceeds by C-to-U conversions at specific sites. Nuclear-encoded factors are required for the recognition of cis -elements located immediately upstream of editing sites. The ensemble of editing sites in a chloroplast genome differs widely between species, and editing sites are thought to evolve rapidly. However, large-scale analyses of the evolution of individual editing sites have not yet been undertaken. 相似文献8.
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Konstantinos P Exarchos Themis P Exarchos Georgios Rigas Costas Papaloukas Dimitrios I Fotiadis 《BMC bioinformatics》2011,12(1):142
Background
In peptides and proteins, only a small percentile of peptide bonds adopts the cis configuration. Especially in the case of amide peptide bonds, the amount of cis conformations is quite limited thus hampering systematic studies, until recently. However, lately the emerging population of databases with more 3D structures of proteins has produced a considerable number of sequences containing non-proline cis formations (cis-nonPro). 相似文献13.
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