Chromosomal Proximity of Genes as an Indicator of Functional Linkage
Mostly prokaryotic genes have a tendency to be organized as clusters across chromosomes. Chromosomal proximity of genes, irrespective of the relative gene orientation, has been shown to be an indicative of their co-regulation. Genes that participate in related biological processes are often observed to be co-regulated. Hence, chromosomal proximity of genes has been proposed as a parameter indicative of functional linkages between them. However, prokaryotic genomes have been subjected to random rearrangements during evolution but these rearrangements are conservative in nature which invariably maintain individual genes in very specific functional and regulatory contexts. Hence, it is possible to deduce these rearrangements of genes based on chromosomal proximity of orthologous genes in multiple reference genomes. This chapter introduces the concept of genomic re-arrangements and discusses chromosomal proximity based three protein–protein interaction prediction methods.
- 3.Beckwith, J.: The operon as paradigm: normal science and the beginning of biological complexity. J. Mol. Biol. 409(1), 7–13 (2011)Google Scholar
- 6.Keseler, I.M., et al.: EcoCyc: a comprehensive view of Escherichia coli biology. Nucleic Acids Res. 37(Database issue), D464–D470 (2009)Google Scholar
- 17.Makarova, K.S., et al.: Defense islands in bacterial and archaeal genomes and prediction of novel defense systems. J Bacteriol. 193(21), 6039–6056 (2011)Google Scholar
- 18.Makarova, K.S., et al.: Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9(6), 467–477 (2011)Google Scholar
- 19.Jensen, L.J., et al.: STRING 8—a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37(Database issue), D412–D416 (2009)Google Scholar
- 34.Ferrer, L., Dale, J.M., Karp, P.D.: A systematic study of genome context methods: calibration, normalization and combination. BMC Bioinform. 11, 493 (2010)Google Scholar