Evolutionary anatomies of positions and types of disease-associated and neutral amino acid mutations in the human genome

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Subramanian, Sankar ^a,b   Kumar, Sudhir ^a  

^a ARIZONA STATE UNIVERSITY   (United States)

^b MASSEY UNIVERSITY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; DISEASE ASSOCIATION; GENE CLUSTER; GENE FREQUENCY; GENE MUTATION; GENE SEQUENCE; GENETIC CONSERVATION; GENOME ANALYSIS; GENOTYPE; HUMAN; MOLECULAR EVOLUTION; NATURAL SELECTION; NONHUMAN; PATHOGENESIS; POPULATION GENETICS; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES DIFFERENCE;

AMINO ACID SUBSTITUTION; ANIMALS; CHICKENS; EVOLUTION, MOLECULAR; GENE FREQUENCY; GENETIC DISEASES, INBORN; GENOME, HUMAN; HUMANS; MICE; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; TAKIFUGU;

VERTEBRATA;

EID: 33845894704     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-306     Document Type: Article

References (28)

1. Pauling L, Itano HA, et al.: Sickle cell anemia a molecular disease. Science 1949, 110(2865):543-548.
2. Cooper DN, Ball EV, Krawczak M: The human gene mutation database. Nucleic Acids Res 1998, 26(1):285-287.
3. Miller MP, Kumar S: Understanding human disease mutations through the use of interspecific genetic variation. Hum Mol Genet 2001, 10(21):2319-2328.
4. Miller MP, Parker JD, Rissing SW, Kumar S: Quantifying the intragenic distribution of human disease mutations. Ann Hum Genet 2003, 67(Pt 6):567-579.
5. Briscoe AD, Gaur C, Kumar S: The spectrum of human rhodopsin disease mutations through the lens of interspecific variation. Gene 2004, 332:107-118.
6. Mooney SD, Klein TE: The functional importance of disease-associated mutation. BMC Bioinformatics 2002, 3:24.
7. Ng PC, Henikoff S: Predicting deleterious amino acid substitutions. Genome Res 2001, 11 (5):863-874.
8. Ng PC, Henikoff S: SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 2003, 31(13):3812-3814.
9. Sunyaev S, Ramensky V, Koch I, Lathe W 3rd, Kondrashov AS, Bork P: Prediction of deleterious human alleles. Hum Mol Genet 2001, 10(6):591-597.
10. Tang H, Wyckoff GJ, Lu J, Wu CI: A universal evolutionary index for amino acid changes. Mol Biol Evol 2004, 21(8):1548-1556.
11. Kondrashov AS, Sunyaev S, Kondrashov FA: Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci U S A 2002, 99(23):14878-14883.
12. Waterston RH, Lindblad-Toh K. Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Einitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L. Grafham D, Graves TA, Green ED, Gregory S, Guigo R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M. Jones TA, Joy A. Kamal M, et al.: Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420(6915):520-562.
13. Gao L, Zhang J: Why are some human disease-associated mutations fixed in mice? Trends Genet 2003, 19(12):678-681.
14. Capriotti E, Calabrese R, Casadio R: Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 2006, 22(22):2729-2734.
15. Sunyaev S, Hanke J, Aydin A. Wirkner U, Zastraw I, Reich J, Bork P: Prediction of nonsynonymous single nucleotide polymophisms in human disease-associated genes. J Mol Med 1999, 77(11):754-760.
16. Kondrashov FA, Ogurtsov AY, Kondrashov AS: Bioinformatical assay of human gene morbidity. Nucleic Acids Res 2004, 32(5):1731-1737.
17. Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13(5):555-556.
18. Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8(3):275-282.
19. Grantham R: Amino acid difference formula to help explain protein evolution. Science 1974, 185(4154):862-864.
20. Jimenez-Sanchez G, Childs B, Valle D: Human disease genes. Nature 2001, 409(6822):853-855.
21. Kulathinal RJ, Bettencourt BR, Hard DL: Compensated deleterious mutations in insect genomes. Science 2004, 306(5701):1553-1554.
22. Ferrer-Costa C, Orozco M, Cruz XD: Characterization of Compensated Mutations in Terms of Structural and Physico-Chemical Properties. J Mol Biol 2006.
23. GenBank (Build 34.1) [ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/ BUILD.34.1/]
24. ENSEMBLE [http://www.ensembl.org]
25. Altschul SF, Gish W, Miller W, Myers EW, Upman DJ: Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
26. Subramanian S, Kumar S: Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 2004, 168(1):373-381.
27. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22(22):4673-4680.
28. HGMD [http://archive.uwcm.ac.uk/uwcm/mg/hgmdO.html]