Testing the ortholog conjecture with comparative functional genomic data from mammals

PLoS Computational Biology

Volumn 7, Issue 6, 2011, Pages

  Nehrt, Nathan L ^a   Clark, Wyatt T ^a   Radivojac, Predrag ^a   Hahn, Matthew W ^a,b  

^a INDIANA UNIVERSITY   (United States)

^b INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FORECASTING; GENES; PROTEINS;

COMPARATIVE GENOMICS; FUNCTIONAL GENOMICS; FUNCTIONAL SIMILARITY; GENOMIC DATA; LARGE SCALE TESTS; ORTHOLOGOUS GENES; ORTHOLOGS; PARALOGOUS GENES; PARALOGS; PROTEIN FUNCTIONS;

MAMMALS;

ARTICLE; CHROMOSOME; CONTROLLED STUDY; DATA ANALYSIS; FUNCTIONAL GENOMICS; GENE CONVERSION; GENE DUPLICATION; GENE FUNCTION; GENE LOCATION; GENE SEQUENCE; GENETIC DIFFERENCE; GENETIC VARIABILITY; HUMAN VERSUS ANIMAL COMPARISON; MAMMALIAN GENETICS; MICROARRAY ANALYSIS; ORTHOLOGY; PARALOGY; PREDICTION; PROTEIN FUNCTION; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; STRUCTURE ACTIVITY RELATION; SYSTEMATIC ERROR; ANIMAL; COMPARATIVE GENOMIC HYBRIDIZATION; DNA MICROARRAY; GENE; GENE DOSAGE; GENE EXPRESSION PROFILING; GENETICS; HUMAN; MOLECULAR EVOLUTION; MOUSE;

MAMMALIA;

PROTEIN;

ANIMALS; COMPARATIVE GENOMIC HYBRIDIZATION; EVOLUTION, MOLECULAR; GENE DOSAGE; GENE EXPRESSION PROFILING; GENES; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEINS;

EID: 79959828326     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002073     Document Type: Article

References (56)

1. Bridges CB, (1935) Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. Journal of Heredity 26: 60-64.
2. Bridges CB, (1936) The Bar "gene" a duplication. Science 83: 210-211.
3. Muller HJ, (1936) Bar duplication. Science 83: 528-530.
4. Stephens SG, (1951) Possible significance of duplication in evolution. Advances in Genetics 4: 247-265.
5. Ohno S, (1970) Evolution by Gene Duplication. Berlin Springer-Verlag.
6. Hahn MW, (2009) Distinguishing among evolutionary models for the maintenance of gene duplicates. Journal of Heredity 100: 605-617.
7. Zuckerkandl E, Pauling L, (1965) Evolutionary divergence and convergence in proteins. In: Bryson V, Vogel HJ, editors. Evolving Genes and Proteins New York Academic Press pp. 97-166.
8. Fitch WM, (1970) Distinguishing homologous from analogous proteins. Systematic Zoology 19: 99-113.
9. Fitch WM, (2000) Homology: a personal view on some of the problems. Trends in Genetics 16: 227-231.
10. Tatusov RL, Koonin EV, Lipman DJ, (1997) A genomic perspective on protein families. Science 278: 631-637.
11. Chen RD, Jeong SS, (2000) Functional prediction: Identification of protein orthologs and paralogs. Protein Science 9: 2344-2353.
12. Dolinski K, Botstein D, (2007) Orthology and functional conservation in eukaryotes. Annual Review of Genetics 41: 465-507.
13. Eisen JA, (1998) Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Research 8: 163-167.
14. Hulsen T, Huynen MA, de Vlieg J, Groenen PMA, (2006) Benchmarking ortholog identification methods using functional genomics data. Genome Biology 7.
15. Koonin EV, (2005) Orthologs, paralogs, and evolutionary genomics. Annual Review of Genetics 39: 309-338.
16. Lee D, Redfern O, Orengo C, (2007) Predicting protein function from sequence and structure. Nature Reviews Molecular Cell Biology 8: 995-1005.
17. Zmasek CM, Eddy SR, (2002) RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs. BMC Bioinformatics 3.
18. Engelhardt BE, Jordan MI, Muratore KE, Brenner SE, (2005) Protein molecular function prediction by Bayesian phylogenomics. PLoS Computational Biology 1: 432-445.
19. Studer RA, Robinson-Rechavi M, (2009) How confident can we be that orthologs are similar, but paralogs differ? Trends in Genetics 25: 210-216.
20. Goodman M, Moore GW, Matsuda G, (1975) Darwinian evolution in genealogy of hemoglobin. Nature 253: 603-608.
21. Kimura M, (1981) Was globin evolution very rapid in its early stages: a dubious case against the rate-constancy hypothesis. Journal of Molecular Evolution 17: 110-113.
22. Li WH, Gojobori T, (1983) Rapid evolution of goat and sheep globin genes following gene duplication. Molecular Biology and Evolution 1: 94-108.
23. Lynch M, Conery JS, (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
24. Des Marais DL, Rausher MD, (2008) Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 454: 762-765.
25. Han MV, Demuth JP, McGrath CL, Casola C, Hahn MW, (2009) Adaptive evolution of young duplicated genes in mammals. Genome Research 19: 859-867.
26. Studer RA, Penel S, Duret L, Robinson-Rechavi M, (2008) Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Research 18: 1393-1402.
27. Tennessen JA, (2008) Positive selection drives a correlation between non-synonymous/synonymous divergence and functional divergence. Bioinformatics 24: 1421-1425.
28. Gabaldon T, (2008) Large-scale assignment of orthology: back to phylogenetics? Genome Biology 9: 235.
29. Kuzniar A, van Ham R, Pongor S, Leunissen JAM, (2008) The quest for orthologs: finding the corresponding gene across genomes. Trends in Genetics 24: 539-551.
30. Sennblad B, Lagergren J, (2009) Probabilistic orthology analysis. Systematic Biology 58: 411-424.
31. Alexeyenko A, Tamas I, Liu G, Sonnhammer ELL, (2006) Automatic clustering of orthologs and inparalogs shared by multiple proteomes. Bioinformatics 22: E9-E15.
32. Datta RS, Meacham C, Samad B, Neyer C, Sjolander K, (2009) Berkeley PHOG: PhyloFacts orthology group prediction web server. Nucleic Acids Research 37: W84-W89.
33. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, et al. (2009) EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Research 19: 327-335.
34. Gabaldon T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer ELL, et al. (2009) Joining forces in the quest for orthologs. Genome Biology 10: 403.
35. Sonnhammer ELL, Koonin EV, (2002) Orthology, paralogy and proposed classification for paralog subtypes. Trends in Genetics 18: 619-620.
36. Han MV, Hahn MW, (2009) Identifying parent-daughter relationships among duplicated genes. Pacific Symposium on Biocomputing 14: 114-125.
37. McGrath CL, Casola C, Hahn MW, (2009) Minimal effect of ectopic gene conversion among recent duplicates in four mammalian genomes. Genetics 182: 615-622.
38. Zhang ZD, Burch PE, Cooney AJ, Lanz RB, Pereira FA, et al. (2004) Genomic analysis of the nuclear receptor family: New insights into structure, regulation, and evolution from the rat genome. Genome Research 14: 580-590.
39. Katz P, Whalen G, Kehri JH, (1994) Differential expression of a novel protein kinase in human B lymphocytes. Preferential localization in the germinal center. Journal of Biological Chemistry 269: 16802-16809.
40. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proceedings of the National Academy of Sciences of the United States of America 101: 6062-6067.
41. Makova KD, Li WH, (2003) Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Research 13: 1638-1645.
42. Liao BY, Zhang JZ, (2006) Evolutionary conservation of expression profiles between human and mouse orthologous genes. Molecular Biology and Evolution 23: 530-540.
43. Huminiecki L, Wolfe KH, (2004) Divergence of spatial gene expression profiles following species-specific gene duplications in human and mouse. Genome Research 14: 1870-1879.
44. Rentzsch R, Orengo CA, (2009) Protein function prediction- the power of multiplicity. Trends in Biotechnology 27: 210-219.
45. Addou S, Rentzsch R, Lee D, Orengo CA, (2009) Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer. Journal of Molecular Biology 387: 416-430.
46. Rost B, Liu J, Nair R, Wrzeszczynski KO, Ofran Y, (2003) Automatic prediction of protein function. Cellular and Molecular Life Sciences 60: 2637-2650.
47. Hawkins T, Luban S, Kihara D, (2006) Enhanced automated function prediction using distantly related sequences and contextual association by PFP. Protein Science 15: 1550-1556.
48. Martin DM, Berriman M, Barton GJ, (2004) GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC Bioinformatics 5: 178.
49. Mika S, Rost B, (2006) Protein-protein interactions more conserved within species than across species. PLoS Computational Biology 2: e79.
50. Liao BY, Zhang JZ, (2008) Null mutations in human and mouse orthologs frequently result in different phenotypes. Proceedings of the National Academy of Sciences of the United States of America 105: 6987-6992.
51. Li W-H, (1997) Molecular Evolution. Sunderland, Mass. Sinauer Associates.
52. Schnoes AM, Brown SD, Dodevski I, Babbitt PC, (2009) Annotation error in public databases: Misannotation of molecular function in enzyme superfamilies. PLoS Computational Biology 5: e1000605.
53. Shi G, Zhang L, Jiang T, (2010) MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. BMC Bioinformatics 11: 10.
54. Goldman N, Yang ZH, (1994) Codon-based model of nucleotide substitution for protein-coding DNA sequences. Molecular Biology and Evolution 11: 725-736.
55. Radivojac P, Peng K, Clark WT, Peters BJ, Mohan A, et al. (2008) An integrated approach to inferring gene-disease associations in humans. Proteins-Structure Function and Bioinformatics 72: 1030-1037.
56. Glazko G, Gordon A, Mushegian A, (2005) The choice of optimal distance measure in genome-wide datasets. Bioinformatics 21: iii3-iii11.