SpringerProtocols: Abstract: Inferring Functional Relationships from Conservation of Gene Order

8. Inferring Functional Relationships from Conservation of Gene Order

By: Gabriel Moreno-Hagelsieb³

Abstract

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The idea behind the gene neighbor method is that conservation of gene order in evolutionarily distant prokaryotes indicates functional association. The procedure presented here starts with the organization of all the genomes into pairs of adjacent genes. Then, pairs of genes in a genome of interest are mapped to their corresponding orthologs in other, informative, genomes. The final step is to determine whether the orthologs of each original pair of genes are also adjacent in the informative genome.

Affiliation(s): (3) Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada

Book Title: Bioinformatics: Structure, Function and Applications

Series: Methods in Molecular Biology | Volume: 453 | Pub. Date: May-01-2008 | Page Range: 181-199 | DOI: 10.1007/978-1-60327-429-6_8

Subject: Bioinformatics

Key Words: Conservation of gene order - operon - genomic context - functional inference - gene neighbor method

References

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1.	Dandekar, T., Snel, B., Huynen, M., et al. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23, 324–328.

2.	Overbeek, R., Fonstein, M., D'Souza, M., et al. (1999) Use of contiguity on the chromosome to predict functional coupling. In Silico Biol 1, 93–108.

3.	Overbeek, R., Fonstein, M., D'Souza, M., et al. (1999) The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A 96, 2896–2901.

4.	Jacob, F., Perrin, D., Sanchez, C., et al. (1960) [Operon: a group of genes with the expression coordinated by an operator.]. C R Hebd Seances Acad Sci 250, 1727–1729.

5.	Jacob, F., Perrin, D., Sanchez, C., et al. (2005) [The operon: a group of genes with expression coordinated by an operator.] Comptes rendus biologies 328, 514–520.

6.	Mushegian, A. R., Koonin, E. V. (1996) Gene order is not conserved in bacterial evolution. Trends Genet 12, 289–290.

7.	Bork, P. , Dandekar, T., Diaz-Lazcoz, Y., et al. (1998) Predicting function: from genes to genomes and back. J Mol Biol 283, 707–725.

8.	Korbel, J. O., Jensen, L. J., von Mering, C., et al. (2004) Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol 22, 911–917.

9.	Ermolaeva, M. D., White, O., Salzberg, S. L. (2001) Prediction of operons in microbial genomes. Nucleic Acids Res 29, 1216–1221.

10.	Janga, S. C., Moreno-Hagelsieb, G. (2004) Conservation of adjacency as evidence of paralogous operons. Nucleic Acids Res 32, 5392–5397.

11.	Snel, B., Lehmann, G., Bork, P., et al. (2000) STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res 28, 3442–3444.

12.	von Mering, C., Huynen, M., Jaeggi, D., et al. (2003) STRING: a database of predicted functional associations between proteins. Nucleic Acids Res 31, 258–261.

13.	Zheng, Y., Anton, B. P., Roberts, R. J., et al. (2005) Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics 6, 243.

14.	Maglott, D. R., Katz, K. S., Sicotte, H., et al. (2000) NCBI's LocusLink and RefSeq. Nucleic Acids Res 28, 126–128.

15.	Pruitt, K. D., Tatusova, T., Maglott, D. R. (2005) NCBI Reference Sequence (Ref-Seq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 33, D501–504.

16.	Altschul, S. F., Madden, T. L., Schaffer, A. A., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.

17.	Fitch, W. M. (2000) Homology a personal view on some of the problems. Trends Genet 16, 227–231.

18.	Gevers, D., Vandepoele, K., Simillion, C., et al. (2004) Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol 12, 148–154.

19.	Schaffer, A. A., Aravind, L., Madden, T. L., et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 29, 2994–3005.

20.	Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474.

21.	Salgado, H., Gama-Castro, S., Peralta-Gil, M., et al. (2006) RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res 34, D394–397.

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