Detection of biochemical pathways by probabilistic matching of phyletic vectors

PLoS ONE

Volumn 4, Issue 4, 2009, Pages

  Li, Hua ^a   Kristensen, David M ^a   Coleman, Michael K ^a   Mushegian, Arcady ^a,b  

^a STOWERS INSTITUTE FOR MEDICAL RESEARCH   (United States)

^b UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; CELL ENZYME;

ARTICLE; BACTERIAL GENOME; CARBON SOURCE; CELL INTERACTION; CELL MOTILITY; CELL SECRETION; CELL SURFACE; CLUSTER ANALYSIS; CONTROLLED STUDY; ENERGY METABOLISM; ENZYME SYNTHESIS; GENE FUNCTION; GENE REGULATORY NETWORK; GENE VECTOR; GENETIC ALGORITHM; GENETIC DIFFERENCE; GENETIC SIMILARITY; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; NONHUMAN; ORTHOLOGY; PROBABILITY; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN SYNTHESIS; SENSITIVITY AND SPECIFICITY; ALGORITHM; BIOLOGY; GENOME; METHODOLOGY; PHYLOGENY;

PROKARYOTA;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOME; PHYLOGENY;

EID: 65449187899     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005326     Document Type: Article

References (29)

1. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278(5338): 631-7.
2. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA 96: 4285-4288.
3. Glazko GV, Mushegian AR (2004) Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns. Genome Biol 5: R32.
4. Wu J, Kasif S, DeLisi C (2003) Identification of functional links between genes using phylogenetic profiles. Bioinformatics 19(12): 1524-30.
5. Wu J, Mellor JC, DeLisi C (2005) Deciphering protein network organization using phylogenetic profile groups. Genome Inform 16(1): 142-9.
6. Goh C, Liu Y, Li J, Lussier Y, Gerstein M (2006) Integration of curated databases to identify genotype-phenotype associations. BMC Genomics 7: e257.
7. Jothi R, Przytycka TM, Aravind L (2007) Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 8: 173.
8. Levesque M, Shasha D, Kim W, Surette MG, Benfey PN (2003) Trait-to-gene: a computational method for predicting the function of uncharacterized genes. Curr Biol 13: 129-133.
9. Jim K, Parmar K, Singh M, Tavazoie S (2004) A Cross-Genomic Approach for Systematic Mapping of Phenotypic Traits to Genes. Genome Research 14: 109-115.
10. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, et al. (2007) STRING 7 - Recent developments in the integration and prediction of protein interactions. Nucleic Acids Research 35.
11. Papp B, Pal C, Hurst LD (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 10;429(6992): 661-4.
12. Koonin EV, Mushegian AR, Bork P (1996) Non-orthologous gene displacement. Trends Genet 12: 334-336.
13. Snel B, Bork P, Huynen MA (2002) Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res 12(1): 17-25.
14. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
15. Glazko G, Coleman M, Mushegian A (2006) Similarity searches in genome-wide numerical data sets. Biology Direct 1: 13.
16. Brandt U (2006) Energy converting NADH:quinone oxidoreductase (complex I). Annual Review of Biochemistry 75: 69-92.
17. Liu R, Ochman H (2007) Stepwise formation of the bacterial flagellar system. Proc Natl Acad Sci U S A 2007, 104(17): 7116-21.
18. Sadreyev R, Grishin N (2003) COMPASS: A tool for comparison of multiple protein alignments with assessment of statistical significance. Journal of Molecular Biology 326 (1): 317-336.
19. Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry. W. H. Freeman.
20. Filloux A, Hachani A, Bleves S (2008) The bacterial type VI secretion machine: yet another player for protein transport across membranes. Microbiology 154: 1570-83.
21. Bingle LE, Bailey CM, Pallen MJ (2008) Type VI secretion: a beginner's guide. Curr Opin Microbiol 11(1): 3-8.
22. Forterre P (2002) A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein. Trends Genetics 18: 236-237.
23. Romero H, Zhang Y, Gladyshev VN, Salinas G (2005) Evolution of selenium utilization traits. Genome Biol 6: R66.
24. Bardy SL, Ng SY, Jarrell KF (2003) Prokaryotic motility structures. Microbiology 149: 295-304.
25. Brochier-Armanet C, Forterre P (2007) Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2: 83-93.
26. Korbel JO, Doerks T, Jensen LJ, Perez-Iratxeta C, Kaczanowski S, et al. (2005) Systematic association of genes to phenotypes by genome and literature mining. PLoS Biol 3: 815-825.
27. Kensche PR, van Noort V, Dutilh BE, Huynen MA (2008) Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface 5(19): 151-70.
28. Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC (2006) The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. Nucleic Acids Res 34: D332-D334.
29. Glazko G, Gordon A, Mushegian A (2005) The choice of optimal distance measure in genome-wide data sets. Bioinformatics 21 Suppl 3: iii3-iii11.