All duplicates are not equal: The difference between small-scale and genome duplication

Genome Biology

Volumn 8, Issue 10, 2007, Pages

  Hakes, Luke ^a   Pinney, John W ^a   Lovell, Simon C ^a   Oliver, Stephen G ^a   Robertson, David L ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CONTROLLED STUDY; GENE DELETION; GENE DUPLICATION; GENE FUNCTION; GENETIC DIFFERENCE; GENETIC IDENTIFICATION; GENETIC VARIABILITY; MOLECULAR MECHANICS; NONHUMAN; PARALOGY; PHENOTYPE; PROTEIN FUNCTION; SACCHAROMYCES CEREVISIAE; BIOLOGY; COMPARATIVE STUDY; ESSENTIAL GENE; FUNGAL GENE; GENETIC DATABASE; GENETICS; GENOME;

SACCHAROMYCES CEREVISIAE;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE DUPLICATION; GENES, ESSENTIAL; GENES, FUNGAL; GENOME, FUNGAL; PHENOTYPE; SACCHAROMYCES CEREVISIAE;

EID: 38049133600     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2007-8-10-r209     Document Type: Article

References (50)

1. Nei M Gene duplication and nucleotide substitution in evolution. Nature 1969 221 40-42 10.1038/221040a0 5782607
2. Ohno S Evolution by Gene Duplication London, New York: Allen & Unwin, Springer-Verlag 1970
3. Davis JC Petrov DA Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet 2005 21 548-551 10.1016/ j.tig.2005.07.008 16098632
4. Guan Y Dunham MJ Troyanskaya OG Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics 2007 175 933-943 1800624 17151249 10.1534/genetics.106.064329
5. Gu X Zhang Z Huang W Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc Natl Acad Sci USA 2005 102 707-712 545572 15647348 10.1073/pnas.0409186102
6. Wagner A How the global structure of protein interaction networks evolves. Proc Biol Sci 2003 270 457-466 1691265 12641899 10.1098/ rspb.2002.2269
7. Davis JC Petrov DA Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol 2004 2 E55 368158 15024414 10.1371/ journal.pbio.0020055
8. Gu Z Cavalcanti A Chen FC Bouman P Li WH Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 2002 19 256-262 11861885
9. Jordan IK Wolf YI Koonin EV Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol 2004 4 22 481058 15238160 10.1186/1471-2148-4-22
10. Kondrashov FA Rogozin IB Wolf YI Koonin EV Selection in the evolution of gene duplications. Genome Biol 2002 3 RESEARCH0008 65685 11864370
11. Seoighe C Wolfe KH Yeast genome evolution in the post-genome era. Curr Opin Microbiol 1999 2 548-554 10.1016/S1369-5274(99)00015-6 10508730
12. Wen-Hsiung L Graur D Fundamentals of Molecular Evolution Sunderland, MA, USA: Sineaur Associates 1999
13. Giot L Bader JS Brouwer C Chaudhuri A Kuang B Li Y Hao YL Ooi CE Godwin B Vitols E et al. A protein interaction map of Drosophila melanogaster. Science 2003 302 1727-1736 10.1126/science.1090289 14605208
14. Ito T Chiba T Ozawa R Yoshida M Hattori M Sakaki Y A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci USA 2001 98 4569-4574 31875 11283351 10.1073/pnas.061034498
15. Ito T Ota K Kubota H Yamaguchi Y Chiba T Sakuraba K Yoshida M Roles for the two-hybrid system in exploration of the yeast protein interactome. Mol Cell Proteomics 2002 1 561-566 10.1074/mcp.R200005-MCP200 12376571
16. Uetz P Giot L Cagney G Mansfield TA Judson RS Knight JR Lockshon D Narayan V Srinivasan M Pochart P et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000 403 623-627 10.1038/35001009 10688190
17. Tong AH Lesage G Bader GD Ding H Xu H Xin X Young J Berriz GF Brost RL Chang M et al. Global mapping of the yeast genetic interaction network. Science 2004 303 808-813 10.1126/science.1091317 14764870
18. Gavin AC Bosche M Krause R Grandi P Marzioch M Bauer A Schultz J Rick JM Michon AM Cruciat CM et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 2002 415 141-147 10.1038/415141a 11805826
19. Ho Y Gruhler A Heilbut A Bader GD Moore L Adams SL Millar A Taylor P Bennett K Boutilier K et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 2002 415 180-183 10.1038/415180a 11805837
20. Krogan NJ Peng WT Cagney G Robinson MD Haw R Zhong G Guo X Zhang X Canadien V Richards DP et al. High-definition macromolecular composition of yeast RNA-processing complexes. Mol Cell 2004 13 225-239 10.1016/ S1097-2765(04)00003-6 14759368
21. Kellis M Birren BW Lander ES Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 2004 428 617-624 10.1038/nature02424 15004568
22. Vazquez A Flammini A Maritan A Vespignani A Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 2003 21 697-700 10.1038/nbt825 12740586
23. Rives AW Galitski T Modular organization of cellular networks. Proc Natl Acad Sci USA 2003 100 1128-1133 298738 12538875 10.1073/pnas.0237338100
24. Wagner A Asymmetric functional divergence of duplicate genes in yeast. Mol Biol Evol 2002 19 1760-1768 12270902
25. Baudot A Jacq B Brun C A scale of functional divergence for yeast duplicated genes revealed from analysis of the protein-protein interaction network. Genome Biol 2004 5 R76 545596 15461795 10.1186/ gb-2004-5-10-r76
26. Conant GC Wolfe KH Functional partitioning of yeast co-expression networks after genome duplication. PLoS Biol 2006 4 e109 1420641 16555924 10.1371/journal.pbio.0040109
27. Ashburner M Ball CA Blake JA Botstein D Butler H Cherry JM Davis AP Dolinski K Dwight SS Eppig JT Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000 25 25-29 10.1038/ 75556 10802651
28. Jiang JJ Conrath DW Semantic Similarity based on Corpus Statistics and Lexical Taxonomy Taiwan: ROCLING X 1998
29. Lin D An information-theoretic definition of similarity. http://www.cs.ualberta.ca/lindek/papers/sim.pdf
30. Resnik P Semantic similarity in a taxonomy: An information-based measure and its application to problems of ambiguity in natural language. J Artificial Intelligence Res 1999 11 95-130
31. Cornell M Paton NW Oliver SG A critical and integrated view of the yeast interactome. Comparative Functional Genomics 2004 382-402 10.1002/cfg.412
32. Harris MA Clark J Ireland A Lomax J Ashburner M Foulger R Eilbeck K Lewis S Marshall B Mungall C et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004 32 Database D258-D261 308770 14681407
33. Lord PW Stevens RD Brass A Goble CA Investigating semantic similarity measures across the Gene Ontology: The relationship between sequence and annotation. Bioinformatics 2003 19 1275-1283 10.1093/bioinformatics/ btg153 12835272
34. Saccharomyces Gene Deletion Project http://www-sequence.stanford.edu/ group/yeast_deletion_project/deletions3.html
35. Gu Z Steinmetz LM Gu X Scharfe C Davis RW Li WH Role of duplicate genes in genetic robustness against null mutations. Nature 2003 421 63-66 10.1038/nature01198 12511954
36. Veitia RA Exploring the etiology of haploinsufficiency. Bioessays 2002 24 175-184 10.1002/bies.10023 11835282
37. Papp B Pal C Hurst LD Dosage sensitivity and the evolution of gene families in yeast. Nature 2003 424 194-197 10.1038/nature01771 12853957
38. Mewes HW Frishman D Mayer KF Munsterkotter M Noubibou O Pagel P Rattei T Oesterheld M Ruepp A Stumpflen V MIPS: Analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 2006 34 D169-172 1347510 16381839 10.1093/nar/gkj148
39. Rottensteiner H Kal AJ Hamilton B Ruis H Tabak HF A heterodimer of the Zn2Cys6 transcription factors Pip2p and Oaf1p controls induction of genes encoding peroxisomal proteins in Saccharomyces cerevisiae. Eur J Biochem 1997 247 776-783 10.1111/j.1432-1033.1997.00776.x 9288897
40. Bray D Lay S Computer-based analysis of the binding steps in protein complex formation. Proc Natl Acad Sci USA 1997 94 13493-13498 28333 9391053 10.1073/pnas.94.25.13493
41. Deutschbauer AM Jaramillo DF Proctor M Kumm J Hillenmeyer ME Davis RW Nislow C Giaever G Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics 2005 169 1915-1925 1449596 15716499 10.1534/genetics.104.036871
42. Aury JM Jaillon O Duret L Noel B Jubin C Porcel BM Segurens B Daubin V Anthouard V Aiach N Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature 2006 444 171-178 10.1038/ nature05230 17086204
43. Lynch M Conery JS The evolutionary fate and consequences of duplicate genes. Science 2000 290 1151-1155 10.1126/science.290.5494.1151 11073452
44. Wolfe KH Shields DC Molecular evidence for an ancient duplication of the entire yeast genome. Nature 1997 387 708-713 10.1038/42711 9192896
45. Conant GC Wagner A GenomeHistory: A software tool and its application to fully sequenced genomes. Nucleic Acids Res 2002 30 3378-3386 137074 12140322 10.1093/nar/gkf449
46. Yang Z Nielsen R Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 2000 17 32-43 10666704
47. Yang Z PAML: A program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997 13 555-556 9367129
48. Stark C Breitkreutz BJ Reguly T Boucher L Breitkreutz A Tyers M BioGRID: a general repository for interaction datasets. Nucleic Acids Res 2006 34 D535-539 1347471 16381927 10.1093/nar/gkj109
49. Adai AT Date SV Wieland S Marcotte EM LGL: Creating a map of protein function with an algorithm for visualizing very large biological networks. J Mol Biol 2004 340 179-190 10.1016/j.jmb.2004.04.047 15184029
50. Berriz GF King OD Bryant B Sander C Roth FP Characterizing gene sets with FuncAssociate. Bioinformatics 2003 19 2502-2504 10.1093/ bioinformatics/btg363 14668247