Covariation of branch lengths in phylogenies of functionally related genes

PLoS ONE

Volumn 4, Issue 12, 2009, Pages 1-9

  Li, Wai Lok Sibon ^a   Rodrigo, Allen G ^a,b  

^a UNIVERSITY OF AUCKLAND   (New Zealand)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN DERIVATIVE;

ACCURACY; ARTICLE; CORRELATION ANALYSIS; COVARIANCE; GENE; GENE FUNCTION; GENE INTERACTION; GENETIC SIMILARITY; GENETIC VARIABILITY; GENOMICS; MOLECULAR EVOLUTION; PHYLOGENETIC TREE; PREDICTION; PROKARYOTE; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; RECEIVER OPERATING CHARACTERISTIC; RIBOSOME; RNA TRANSLATION; STATISTICAL MODEL; ANIMAL; BACTERIUM; GENETIC DATABASE; GENETICS; HUMAN; PHYLOGENY;

PROKARYOTA;

ANIMALS; BACTERIA; DATABASES, GENETIC; GENES; HUMANS; LINEAR MODELS; PHYLOGENY; RIBOSOMES; ROC CURVE;

EID: 77949494823     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008487     Document Type: Article

References (64)

1. Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and Dating with Confidence. PLoS Biology 4: e88.
2. Kishino H, Thorne JL, Bruno WJ (2001) Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution. Mol Biol Evol 18: 352-361
3. Sanderson MJ (2002) Estimating Absolute Rates of Molecular Evolution and Divergence Times: A Penalized Likelihood Approach. Mol Biol Evol 19: 101-109
4. Thorne JL, Kishino H, Painter IS (1998) Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol 15: 1647-1657
5. Gillespie JH (1991) The Causes of Molecular Evolution. New York: Oxford University Press.
6. Bromham L, Penny D (2003) The modern molecular clock. Nat Rev Genet 4: 216-224
7. Yang Z, Nielsen R (2002) Codon-Substitution Models for Detecting Molecular Adaptation at Individual Sites Along Specific Lineages. Mol Biol Evol 19: 908-917
8. Siepel A, Pollard K, Haussler D (2006) New methods for detecting lineage- specific selection. DOI: 10.1007/11732990.
9. Messier W, Stewart CB (1997) Episodic adaptive evolution of primate lysozymes. Nature 385: 151.
10. Ross HA, Rodrigo AG (2002) Immune-Mediated Positive Selection Drives Human Immunodeficiency Virus Type 1 Molecular Variation and Predicts Disease Duration. J Virol 76: 11715-11720
11. Sumiyama K, Saitou N, Ueda S (2002) Adaptive Evolution of the IgA Hinge Region in Primates. Mol Biol Evol 19: 1093-1099
12. Fay JC, Wu CI (2003) Sequence Divergence, Functional Constraint, and Selection in Protein Evolution. Annual Review of Genomics and Human Genetics 4: 213-235
13. Sawyer SL, Wu LI, Emerman M, Malik HS (2005) Positive selection of primate TRIM5 Î6 identifies a critical species-specific retroviral restriction domain. Proceedings of the National Academy of Sciences of the United States of America 102: 2832-2837
14. Woolfe A, Goodson M, Goode DK, Snell P, McEwen GK, et al. (2005) Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol 3: e7.
15. Thorne JL, Kishino H (2002) Divergence Time and Evolutionary Rate Estimation with Multilocus Data. Systematic Biology 51: 689-702
16. Atwell S, Ultsch M, De Vos AM, Wells JA (1997) Structural Plasticity in a Remodeled Protein-Protein Interface. Science 278: 1125-1128
17. Jucovic M, Hartley RW (1996) Protein-Protein Interaction: A Genetic Selection for Compensating Mutations at the Barnase-Barstar Interface. Proceedings of the National Academy of Sciences of the United States of America 93: 2343-2347
18. Pagès S, Bélaïch A, Bélaïch JP, Morag E, Lamed R, et al. (1997) Species- specificity of the cohesin-dockerin interaction between Clostridium thermo- cellum and Clostridium cellulolyticum: Prediction of specificity determinants of the dockerin domain. Proteins: Structure, Function, and Genetics 29: 517-527
19. Pazos F, Helmer-Citterich M, Ausiello G, Valencia A (1997) Correlated mutations contain information about protein-protein interaction. Journal of Molecular Biology 271: 511-523
20. Poumbourios P, Maerz AL, Drummer HE (2003) Functional Evolution of the HIV-1 Envelope Glycoprotein 120 Association Site of Glycoprotein 41. J Biol Chem 278: 42149-42160
21. Juan D, Pazos F, Valencia A (2008) High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. Proceedings of the National Academy of Sciences 105: 934-939
22. Kann MG, Shoemaker BA, Panchenko AR, Przytycka TM (2009) Correlated Evolution of Interacting Proteins: Looking Behind the Mirrortree. Journal of Molecular Biology 385: 91-98
23. Fryxell KJ (1996) The coevolution of gene family trees. Trends in Genetics 12: 364-369
24. Pazos F, Valencia A (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng 14: 609-614
25. Pazos F, Ranea JAG, Juan D, Sternberg MJE (2005) Assessing Protein Co-evolution in the Context of the Tree of Life Assists in the Prediction of the Interactome. Journal of Molecular Biology 352: 1002-1015
26. Gertz J, Elfond G, Shustrova A, Weisinger M, Pellegrini M, et al. (2003) Inferring protein interactions from phylogenetic distance matrices. Bioinfor- matics 19: 2039-2045
27. Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE (2000) Co-evolution of proteins with their interaction partners. Journal of Molecular Biology 299: 283-293
28. Goh CS, Cohen FE (2002) Co-evolutionary Analysis Reveals Insights into Protein-Protein Interactions. Journal of Molecular Biology 324: 177-192
29. Kim WK, Bolser DM, Park JH (2004) Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics 20: 1138-1150
30. Ramani AK, Marcotte EM (2003) Exploiting the Co-evolution of Interacting Proteins to Discover Interaction Specificity. Journal of Molecular Biology 327: 273-284
31. Sato T, Yamanishi Y, Horimoto K, Toh H, Kanehisa M (2003) Prediction of Protein-Protein Interactions from Phylogenetic Trees Using Partial Correlation Coefficient. Genome Informatics 14: 496-497
32. Tan SH, Zhang Z, Ng SK (2004) ADVICE: Automated Detection and Validation of Interaction by Co-Evolution. Nucl Acids Res 32: W69-72
33. Hakes L, Lovell SC, Oliver SG, Robertson DL (2007) Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proceedings of the National Academy of Sciences 104: 7999-8004
34. Fraser HB, Hirsh AE, Steinmetz LM, Scharfe C, Feldman MW (2002) Evolutionary Rate in the Protein Interaction Network. Science 296: 750-752
35. Jordan IK, Marino-Ramirez L, Wolf YI, Koonin EV (2004) Conservation and Coevolution in the Scale-Free Human Gene Coexpression Network. Mol Biol Evol 21: 2058-2070
36. Marin ̃o-Ramírez L, Bodenreider O, Kantz N, Jordan IK (2006) Co-evolutionary Rates of Functionally Related Yeast Genes. Evolutionary Bioinformatics 2006: 295-300
37. Shapiro BJ, Alm EJ (2008) Comparing Patterns of Natural Selection across Species Using Selective Signatures. PLoS Genetics 4: e23.
38. Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, et al. (2005) Functional genomic analysis of the rates of protein evolution. Proceedings of the National Academy of Sciences 102: 5483-5488
39. Wolf Y, Carmel L, Koonin E (2006) Unifying measures of gene function and evolution. Proceedings of the Royal Society B: Biological Sciences 273: 1507-1515
40. Rausher MD, Miller RE, Tiffin P (1999) Patterns of evolutionary rate variation among genes of the anthocyanin biosynthetic pathway. Mol Biol Evol 16: 266-274
41. Lu Y, Rausher MD (2003) Evolutionary Rate Variation in Anthocyanin Pathway Genes. Mol Biol Evol 20: 1844-1853
42. Ritchie ME, Silver J, Oshlack A, Holmes M, Diyagama D, et al. (2007) A comparison of background correction methods for two-colour microarrays. Bioinformatics 23: 2700-2707
43. 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. Nucl Acids Res 25: 3389-3402
44. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574
45. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25: 25-29
46. Leinonen R, Diez FG, Binns D, Fleischmann W, Lopez R, et al. (2004) UniProt archive. Bioinformatics 20: 3236-3237
47. Wu CH, Huang H, Nikolskaya A, Hu Z, Barker WC (2004) The iProClass integrated database for protein functional analysis. Computational Biology and Chemistry 28: 87-96
48. Foley DH (1972) Considerations of Sample and Feature Size. IEEE Transactions on Information Theory 18: 618-626
49. Drummond A, Strimmer K (2001) PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bioinformatics 17: 662-663
50. Guindon S, Gascuel O (2003) A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology 52: 696-704
51. Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. Atlas of Protein Sequences and Structure 5: 345-352
52. Sing T, Sander O, Beerenwinkel N, Lengauer T (2005) ROCR: visualizing classifier performance in R. Bioinformatics 21: 3940-3941
53. Benjamini Y, Hochberg Y (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289-300
54. Xenarios I, Salwinski L, Duan XJ, Higney P, Kim SM, et al. (2002) DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucl Acids Res 30: 303-305
55. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Assigning protein functions by comparative genome analysis: Protein phyloge- netic profiles. PNAS 96: 4285-4288
56. Jothi R, Przytycka T, Aravind L (2007) Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment. BMC Bioinformatics 8: 173.
57. Singh S, Wall DP (2008) Testing the Accuracy of Eukaryotic Phylogenetic Profiles for Prediction of Biological Function. Evolutionary Bioinformatics 4: 217-223
58. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, et al. (1997) The Complete Genome Sequence of Escherichia coli K-12. Science 277: 1453-1462
59. Lecompte O, Ripp R, Thierry J-C, Moras D, Poch O (2002) Comparative analysis of ribosomal proteins in complete genomes: an example of reductive evolution at the domain scale. Nucl Acids Res 30: 5382-5390
60. Mintseris J, Weng Z (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proceedings of the National Academy of Sciences 102: 10930-10935
61. Shakhnovich BE, Deeds E, Delisi C, Shakhnovich E (2005) Protein structure and evolutionary history determine sequence space topology. Genome Res 15: 385-392
62. Gillmor SA, Takeuchi T, Yang SQ, Craik CS, Fletterick RJ (2000) Compromise and accommodation in ecotin, a dimeric macromolecular inhibitor of serine proteases. Journal of Molecular Biology 299: 993-1003
63. Ranwez V, Delsuc F, Ranwez S, Belkhir K, Tilak MK, et al. (2007) OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics. BMC Evolutionary Biology 7: 241.
64. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Res 13: 2498-2504