Conserved genomic neighborhood is a strong but no perfect indicator for a direct interaction of microbial gene products
作者: Robert EschRainer Merkl
作者单位: 1Faculty of Mathematics and Computer Science, University of Hagen, D-58084, Hagen, Germany
2Institute of Biophysics and Physical Biochemistry, University of Regensburg, D-93040, Regensburg, Germany
刊名: BMC Bioinformatics, 2020, Vol.21 (1), pp.318-356
来源数据库: Springer Nature Journal
DOI: 10.1186/s12859-019-3200-z
关键词: Protein-protein interactionComplex formationSequence similarity networkGenome neighborhood networkBinary classifier
英文摘要: Abstract(#br)Background(#br)The order of genes in bacterial genomes is not random; for example, the products of genes belonging to an operon work together in the same pathway. The cotranslational assembly of protein complexes is deemed to conserve genomic neighborhoods even stronger than a common function. This is why a conserved genomic neighborhood can be utilized to predict, whether gene products form protein complexes. Results(#br)We were interested to assess the performance of a neighborhood-based classifier that analyzes a large number of genomes. Thus, we determined for the genes encoding the subunits of 494 experimentally verified hetero-dimers their local genomic context. In order to generate phylogenetically comprehensive genomic neighborhoods, we utilized the tools offered by...
全文获取路径: Springer Nature  (合作)
影响因子:3.024 (2012)