Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs

PLoS Computational Biology

Volumn 9, Issue 5, 2013, Pages

  Chen, Wei Hua ^a   Zhao, Xing Ming ^b   van Noort, Vera ^a   Bork, Peer ^a,c  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b TONGJI UNIVERSITY   (China)

^c MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; DISEASES;

DISEASE GENES; FUNCTIONAL REDUNDANCY; FUNCTIONAL SIMILARITY; GENETIC DISEASE; GENETIC DISORDERS; HUMAN GENETIC DISORDERS; HUMAN POPULATION; MOLECULAR BASIS; PARALOGS; STOCHASTICITY;

GENES;

ARTICLE; CONTROLLED STUDY; GENE DUPLICATION; GENE MUTATION; GENETIC ASSOCIATION; MONOGENIC DISORDER; ORTHOLOGY; PARALOGY; PHENOTYPE;

EID: 84878497749     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003073     Document Type: Article

References (55)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
2. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, et al. (2001) The sequence of the human genome. Science 291: 1304-1351.
3. Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, et al. (2011) Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 12: 745-755.
4. Rosenberg NA, Huang L, Jewett EM, Szpiech ZA, Jankovic I, et al. (2010) Genome-wide association studies in diverse populations. Nat Rev Genet 11: 356-366.
5. Ott J, Kamatani Y, Lathrop M, (2011) Family-based designs for genome-wide association studies. Nat Rev Genet 12: 465-474.
6. Mushegian AR, Bassett DE Jr, Boguski MS, Bork P, Koonin EV, (1997) Positionally cloned human disease genes: patterns of evolutionary conservation and functional motifs. Proc Natl Acad Sci U S A 94: 5831-5836.
7. Domazet-Loso T, Tautz D, (2008) An Ancient Evolutionary Origin of Genes Associated with Human Genetic Diseases. Molecular Biology and Evolution 25: 2699-2707.
8. Dickerson JE, Robertson DL, (2012) On the Origins of Mendelian Disease Genes in Man: The Impact of Gene Duplication. Molecular Biology and Evolution 29: 61-69.
9. Lopez-Bigas N, Ouzounis CA, (2004) Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Research 32: 3108-3114.
10. Tu ZD, Wang L, Xu M, Zhou XH, Chen T, et al. (2006) Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics 7: 31.
11. Cai JJ, Borenstein E, Chen R, Petrov DA, (2009) Similarly strong purifying selection acts on human disease genes of all evolutionary ages. Genome Biology and Evolution 1: 131-144.
12. Cai JJ, Borenstein E, Petrov DA, (2010) Broker genes in human disease. Genome Biol Evol 2: 815-825.
13. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proc Natl Acad Sci U S A 104: 8685-8690.
14. Feldman I, Rzhetsky A, Vitkup D, (2008) Network properties of genes harboring inherited disease mutations. Proc Natl Acad Sci U S A 105: 4323-4328.
15. Forslund K, Schreiber F, Thanintorn N, Sonnhammer EL, (2011) OrthoDisease: tracking disease gene orthologs across 100 species. Brief Bioinform 12: 463-473.
16. Dean EJ, Davis JC, Davis RW, Petrov Da, (2008) Pervasive and persistent redundancy among duplicated genes in yeast. PLoS genetics 4: e1000113.
17. Li J, Yuan Z, Zhang Z, (2010) The cellular robustness by genetic redundancy in budding yeast. PLoS Genet 6: e1001187.
18. Hsiao TL, Vitkup D, (2008) Role of duplicate genes in robustness against deleterious human mutations. PLoS Genet 4: e1000014.
19. Wagner A, (2008) Gene duplications, robustness and evolutionary innovations. BioEssays: news and reviews in molecular, cellular and developmental biology 30: 367-373.
20. Gu X, Zhang Z, Huang W, (2005) Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc Natl Acad Sci U S A 102: 707-712.
21. Chen W-H, Trachana K, Lercher MJ, Bork P, (2012) Younger Genes Are Less Likely to Be Essential than Older Genes, and Duplicates Are Less Likely to Be Essential than Singletons of the Same Age. Molecular Biology and Evolution 29: 1703-1706.
22. Hanada K, Kuromori T, Myouga F, Toyoda T, Shinozaki K, (2009) Increased Expression and Protein Divergence in Duplicate Genes Is Associated with Morphological Diversification. PLoS Genet 5: e1000781.
23. Ge X, Yamamoto S, Tsutsumi S, Midorikawa Y, Ihara S, et al. (2005) Interpreting expression profiles of cancers by genome-wide survey of breadth of expression in normal tissues. Genomics 86: 127-141.
24. Roth R, Hevezi P, Lee J, Willhite D, Lechner S, et al. (2006) Gene expression analyses reveal molecular relationships among 20 regions of the human CNS. neurogenetics 7: 67-80.
25. Hao L, Ge X, Wan H, Hu S, Lercher MJ, et al. (2010) Human functional genetic studies are biased against the medically most relevant primate-specific genes. BMC Evol Biol 10: 316.
26. Yu G, Li F, Qin Y, Bo X, Wu Y, et al. (2010) GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics 26: 976-978.
27. Nehrt NL, Clark WT, Radivojac P, Hahn MW, (2011) Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS Comput Biol 7: e1002073.
28. Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA, et al. (2012) On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol 8: e1002386.
29. Papp B, Pal C, Hurst LD, (2003) Dosage sensitivity and the evolution of gene families in yeast. Nature 424: 194-197.
30. Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, et al. (2010) CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Research 38: D497-501.
31. Makino T, McLysaght A, (2010) Ohnologs in the human genome are dosage balanced and frequently associated with disease. Proc Natl Acad Sci U S A 107: 9270-9274.
32. Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, et al. (2012) A census of human soluble protein complexes. Cell 150: 1068-1081.
33. Elowitz MB, Levine AJ, Siggia ED, Swain PS, (2002) Stochastic gene expression in a single cell. Science 297: 1183-1186.
34. Burga A, Casanueva MO, Lehner B, (2011) Predicting mutation outcome from early stochastic variation in genetic interaction partners. Nature 480: 250-253.
35. Flicek P, Amode MR, Barrell D, Beal K, Brent S, et al. (2010) Ensembl 2011. Nucleic Acids Res 39: D800-D806.
36. McKusick VA, (2007) Mendelian Inheritance in Man and its online version, OMIM. Am J Hum Genet 80: 588-604.
37. Podder S, Ghosh TC, (2011) Insights into the molecular correlates modulating functional compensation between monogenic and polygenic disease gene duplicates in human. Genomics 97: 200-204.
38. Blekhman R, Man O, Herrmann L, Boyko AR, Indap A, et al. (2008) Natural Selection on Genes that Underlie Human Disease Susceptibility. Current biology 18: 883-889.
39. Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, et al. (2008) TreeFam: 2008 Update. Nucleic Acids Research 36: D735-740.
40. Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, et al. (2012) eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res 40: D284-289.
41. Pearson WR, Lipman DJ, (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 85: 2444-2448.
42. Letunic I, Bork P, (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475-478.
43. Zhang H, Gao S, Lercher MJ, Hu S, Chen WH, (2012) EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. Nucleic Acids Res 40: W569-572.
44. Dehal P, Boore JL, (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3: e314.
45. McLysaght A, Hokamp K, Wolfe KH, (2002) Extensive genomic duplication during early chordate evolution. Nat Genet 31: 200-204.
46. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
47. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Research 39: D561-568.
48. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, et al. (2009) Human Protein Reference Database-2009 update. Nucleic Acids Res 37: D767-772.
49. Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, et al. (2004) The Database of Interacting Proteins: 2004 update. Nucleic Acids Res 32: D449-451.
50. Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, et al. (2012) MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40: D857-861.
51. Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, et al. (2012) The IntAct molecular interaction database in 2012. Nucleic Acids Res 40: D841-846.
52. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, et al. (2011) The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39: D698-704.
53. Rual JF, Venkatesan K, Hao T, Hirozane-Kishikawa T, Dricot A, et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature 437: 1173-1178.
54. Wang X, Wei X, Thijssen B, Das J, Lipkin SM, et al. (2012) Three-dimensional reconstruction of protein networks provides insight into human genetic disease. Nat Biotech 30: 159-164.
55. Wang D, Zhang Y, Zhang Z, Zhu J, Yu J, (2010) KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics, proteomics & bioinformatics/Beijing Genomics Institute 8: 77-80.