Discovering local patterns of co - evolution: Computational aspects and biological examples

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Tuller, Tamir ^a,b   Felder, Yifat ^a   Kupiec, Martin ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROBLEMS; COMPUTATIONAL ASPECTS; EVOLUTIONARY TREE; PHYLOGENETIC TREES; PHYSICAL INTERACTIONS; POSITIVE SELECTION; PROTEIN COMPLEXES; SIGNALING PATHWAYS;

ALGORITHMS; BIOINFORMATICS; FUNGI; GENE EXPRESSION; MAMMALS; PROBLEM SOLVING; TREES (MATHEMATICS);

BIOLOGY;

EUKARYOTA; FUNGI; MAMMALIA; PRIMATES;

ALGORITHM; ARTICLE; BIOLOGY; GENE EXPRESSION PROFILING; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE EXPRESSION PROFILING; PHYLOGENY;

EID: 77949512323     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-43     Document Type: Article

References (40)

1. Chena Y, Dokholyan NV. The coordinated evolution of yeast proteins is constrained by functional modularity. Trends in Genetics 2006, 22(8):416-419. 10.1016/j.tig.2006.06.008, 16797778.
2. Wall DP, Hirsh AE, Fraser HB, Kumm J, Giaever G, Eisen MB, Feldman MW. Functional Genomic Analysis of the Rate of Protein Evolution. Proc Natl Acad Sci USA 2005, 102(15):5483-5488. 10.1073/pnas.0501761102, 555735,555735, 15800036.
3. o Rami'rez LM, Bodenreider O, Kantz N, Jordan IK. Co-evolutionary Rates of Functionally Related Yeast Genes. Evolutionary Bioinformatics 2006, 2295-2300.
4. Pazos F, Helmer-Citterich M, Ausiello G, Valencia A. Correlated Mutations Contain Information About Protein-protein Interaction. J Mol Biol 1997, 271:511-523. 10.1006/jmbi.1997.1198, 9281423.
5. Juan D, Pazos F, Valencia A. High-confidence prediction of global interactomes based on genome-wide coevolutionary networks. PNAS 2008, 105(3):934-939. 10.1073/pnas.0709671105, 2242690, 18199838.
6. Tuller T, Kupiec M, Ruppin E. Co-evolutionary Networks of Genes and Cellular Processes Across Fungal Species. Genome Biol 2009, 10(5):R48. 10.1186/gb-2009-10-5-r48, 2718514, 19416514.
7. Wu J, Kasif S, DeLisi C. Identification of functional links between genes using phylogenetic profiles. Bioinformatics 2003, 19:1524-1530. 10.1093/bioinformatics/btg187, 12912833.
8. Snel B, Huynen M. Quantifying modularity in the evolution of biomolecular systems. Genome Res 2004, 14(3):391-397. 10.1101/gr.1969504, 353226, 14993205.
9. Bowers PM, Pellegrini M, Thompson MJ, Fierro J, Yeates TO, Eisenberg D. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biology 2004, 5:R35. 10.1186/gb-2004-5-5-r35, 416471, 15128449.
10. Pazos F, Valencia A. Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Engineering 2001, 14(9):609-614. 10.1093/protein/14.9.609, 11707606.
11. Goh C, Bogan A, Joachimiak M, Walther D, Cohen F. Co-evolution of proteins with their interaction partners. J Mol Biol 2000, 299(2):283-93. 10.1006/jmbi.2000.3732, 10860738.
12. Barker D, Page M. Predicting functional gene links using phylogenetic-statistical analysis of whole genomes. PLoS Comput Biol 2005, 1:24-31.
13. Barker D, Meade A, Page M. Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics 2007, 23:14-20. 10.1093/bioinformatics/btl558, 17090580.
14. Wapinski I, Pfeffer A, Friedman N, Regev A. Natural history and evolutionary principles of gene duplication in fungi. Nature 2007, 449:54-65. 10.1038/nature06107, 17805289.
15. Tuller T, Birin H, Gophna U, Kupiec M, Ruppin E. Reconstructing Ancestral Gene content by Co-Evolution. Genome Res 2009, 20:122-32. 10.1101/gr.096115.109, 19948819.
16. Krylov DM, Wolf YI, Rogozin IB, Koonin EV. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res 2003, 13(10):2229-35. 10.1101/gr.1589103, 403683, 14525925.
17. Ober D, Harms R, Witte L, Hartmann T. Molecular evolution by change of function. Alkaloid-specific homospermidine synthase retained all properties of deoxyhypusine synthase except binding the eIF5A precursor protein. J Biol Chem 2003, 278(15):12805-12812. 10.1074/jbc.M207112200, 12562768.
18. Przytycka T, Jothi R, Aravind L, Lipman D. Differences in evolutionary pressure acting within highly conserved ortholog groups. BMC Evol Biol 2008, 8(208). 2488352, 18637201.
19. Berbee M, Taylor J. The Mycota VIIB:229-245. Berlin: Springer 2001 chap. Systematics and evolution, McLaughlin D, McLaughlin E, Lemke P.
20. MacQueen JB. Some Methods for classification and Analysis of Multivariate Observations. Proceedings of 5-th Berkeley Symposium on Mathematical Statistics and Probability, Berkeley 1967, 1:281-297. University of California Press.
21. Grossmann S, Bauer S, Robinson PN, Vingron M. An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets. RECOMB06 2006, 85-98.
22. 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, Yi JJ, Natale DA. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4(41). 222959, 12969510.
23. Bie TD, Cristianini N, Demuth JP, Hahn MW. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 2006, 22:1269-1271. 10.1093/bioinformatics/btl097, 16543274.
24. Hedges SB, Chen H, Kumar S, Wang DY, Thompson AS, Watanabe H. A genomic timescale for the origin of eukaryotes. BMC Evol Biol 2001, 1(4). 56995, 11580860.
25. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 2003, 31(13):3497-3500. 10.1093/nar/gkg500, 168907, 12824352.
26. Pupko T, Pe'er I, Shamir R, Graur D. A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol 2000, 17:890-896.
27. Yang Z, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 2000, 17:32-43.
28. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13(5):555.
29. Tanay A, Sharan R, Shamir R. Discovering statistically significant biclusters in gene expression data. Bioinformatics 2002, 18:S136-44.
30. Cheng Y, Church G. Biclustering of expression data. Proc 8th Int Conf Intell Syst Mol Biol 2000, 93-103.
31. Benton M, . PCJDonoghue Paleontological evidence to date the tree of life. Mol Biol Evol 2007, 24:26-53. 10.1093/molbev/msl150, 17047029, PCJDonoghue.
32. Jaccard P. The distribution of flora in the alpine zone. The New Phytologist 1912, 11:37-50.
33. Man O, Pilpel Y. Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nature Genetics 2007, 39:415-421. 10.1038/ng1967, 17277776.
34. Wolfe K, Shields D. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 1997, 387(6634):708-13. 10.1038/42711, 9192896.
35. Ohno S. Evolution by gene duplication 1970, New York: Springer-Verlag.
36. Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, de Montigny J, Marck C, Neuve'glise C, Talla E, Goffard N, Frangeu L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame' A, Boyer J, Cattolico L, Confanioleri F, de Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, We'solowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL. Genome evolution in yeasts. Nature 2004, 430:35-44. 10.1038/nature02579, 15229592.
37. Scannell D, Butler G, Wolfe K. Yeast genome evolution-the origin of the species. Yeast 2007, 24(11):929-942. 10.1002/yea.1515, 17621376.
38. Oron E, Tuller T, Li L, Rozovsky N, Yekutieli D, Rencus-Lazar S, Segal D, Chor B, Edgar BA, Chamovitz DA. Genomic analysis of COP9 signalosome function in Drosophila melanogaster reveals a role in temporal regulation of gene expression. Mol Syst Biol 2007, 3:108. 10.1038/msb4100150, 2673709, 17486136.
39. Chamovitz D, Glickmanb M. The COP9 signalosome. Current Biol 2002, 12(7):R232.
40. Singh R, Xu J, Berger B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc Natl Acad Sci USA 2008, 105(35):12763-12768. 10.1073/pnas.0806627105, 2522262,2522262, 18725631.