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Analysis of Genomic Context : Prediction of Functional Associations from Conserved Bidirectionally Transcribed Gene Pairs
Korbel, Jan O.
Jensen, Lars J.
Mering, Christian von
Article from Journal - ilmiah internasional
Nature Biotechnology: The Science and Business of Biotechnology vol. 22 no. 7 (Jul. 2004)
analysis genomic context
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Several widely used methods for predicting functional associations between proteins are based on the systematic analyis of genomic context. Efforts are going to improve these methods and to search for novel aspects in genomes that could be exploited for function prediction. Here we use gene expression data to demonstrates two functional implications of genome organization : 1. chromosal proximity indicates gone coregulation in prokaryotes independent or relative gene orientation 2. adjacent bidirectionally transcibed genes (That is divergently organized coding regions) with conserved gene orientation are strongly coregulated. We further demonstrate that such bidirectionally transcribed gene pairs are functionally associated and derive from this a novel genomic context method that reliably preficts links between > 2,500 pairs of genes in 200 species. Around 650 of these functional associations are supported by other genomic context methods. In most instaces, one gene encodes a transcriptional regulator, and the other a nonregulatory protein. In depth analysis in escherichia coli shows that the vast majority of these regulators both control transcription of the divergently transcribed target gene / operon and auto regulate their own biosynthesis. The method thus enables the prediction of target pocesses and regulatory features for several hundred transcriptional regulators.
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