Using phylogenetic profiles to predict functional relationships

Methods in Molecular Biology

Volumn 804, Issue , 2012, Pages 167-177

  Pellegrini, Matteo ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Coevolution; Coevolving proteins; Comparative genomics; Functional associations; Phylogenetic profiles

Indexed keywords

MULTIPROTEIN COMPLEX; PROTEIN;

ARTICLE; COMPUTER PROGRAM; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PHYLOGENY; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EVOLUTION, MOLECULAR; MULTIGENE FAMILY; MULTIPROTEIN COMPLEXES; PHYLOGENY; PROTEINS; SIGNAL TRANSDUCTION; SOFTWARE; SYSTEMS BIOLOGY;

EID: 84855897926     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-361-5_9     Document Type: Article

References (23)

1. 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 U S A, 96:4285-4288. (Pubitemid 29190328)
2. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res, 25:3389-3402. (Pubitemid 27359211)
3. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics, 4:41.
4. Bowers PM, Cokus SJ, Eisenberg D, Yeates TO. (2004) Use of logic relationships to decipher protein network organization. Science, 306:2246-2249. (Pubitemid 40024459)
5. Date SV, Marcotte EM. (2003) Discovery of uncharacterized cellular systems by genomewide analysis of functional linkages. Nat Biotechnol, 21:1055-1062. (Pubitemid 37064735)
6. Pazos F, Valencia A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng, 14:609-614. (Pubitemid 33086280)
7. Wu J, Kasif S, DeLisi C. (2003) Identification of functional links between genes using phylogenetic profiles. Bioinformatics, 19:1524-1530. (Pubitemid 37038868)
8. Kharchenko P, Chen L, Freund Y, Vitkup D, Church GM. (2006) Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics, 7:177.
9. Liberles DA. (2001) Evaluation of methods for determination of a reconstructed history of gene sequence evolution. Mol Biol Evol, 18:2040-2047. (Pubitemid 33026775)
10. Barker D, Pagel M. (2005) Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput Biol, 1:e3.
11. Barker D, Meade A, Pagel M. (2007) Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics, 23:14-20. (Pubitemid 46017850)
12. Cokus S, Mizutani S, Pellegrini M. (2007) An improved method for identifying functionally linked proteins using phylogenetic profiles. BMC Bioinformatics, 8(Suppl 4):S7.
13. Bar-Joseph Z, Gifford DK, Jaakkola TS. (2001) Fast optimal leaf ordering for hierarchical clustering. Bioinformatics, 17(Suppl 1): S22-S29. (Pubitemid 33793490)
14. Sun J, Li Y, Zhao Z. (2007) Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? Biochem Biophys Res Commun, 353:985-991. (Pubitemid 46080393)
15. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 25:25-29. (Pubitemid 30257031)
16. 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.
17. 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, 5:151-170. (Pubitemid 350274448)
18. Li H, Pellegrini M, Eisenberg D. (2005) Detection of parallel functional modules by comparative analysis of genome sequences. Nat Biotechnol, 23:253-260. (Pubitemid 40255337)
19. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C. (2009) STRING 8 - a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res, 37: D412-D416.
20. Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. (2004) Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol, 5:R35.
21. Date SV, Marcotte EM. (2005) Protein function prediction using the Protein Link EXplorer (PLEX). Bioinformatics, 21:2558-2559. (Pubitemid 40731628)
22. Hu Z, Hung JH, Wang Y, Chang YC, Huang CL, Huyck M, DeLisi C. (2009) VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. Nucleic Acids Res, 37:W115-W121.
23. Dandekar T, Snel B, Huynen M, Bork P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci, 23:324-328. (Pubitemid 28461862)