The effects of multiple features of alernatively spliced exons on the KAIKS ratio test

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Chen, Feng Chi ^a,b   Chuang, Trees Juen ^a  

^a GENOMICS RESEARCH CENTER   (Taiwan)

^b NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ADDITIVE EFFECTS; COMPLEX CONDITION; DOMINANT FACTOR; FUNCTIONAL DIVERSITY; MULTIPLE FACTORS; MULTIPLE FEATURES; PROTEIN DOMAINS; SPLICING ENHANCER;

PROTEINS;

STATISTICAL TESTS;

RNA; MESSENGER RNA; PROTEIN;

ALTERNATIVE RNA SPLICING; ARTICLE; CELL LINEAGE; COMPUTER PROGRAM; DATA ANALYSIS; ENHANCER REGION; EXON; GENETIC ANALYSIS; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC VARIABILITY; HUMAN; INFORMATION PROCESSING; MATHEMATICAL ANALYSIS; MOUSE; NONHUMAN; ORTHOLOGY; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; SPECIES DIFFERENCE; ANIMAL; BIOLOGICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; GENETICS; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PROTEIN TERTIARY STRUCTURE; RNA SPLICING; SEQUENCE ALIGNMENT;

ALTERNATIVE SPLICING; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; DATABASES, GENETIC; ENHANCER ELEMENTS (GENETICS); EVOLUTION, MOLECULAR; EXONS; HUMANS; MICE; MODELS, GENETIC; PROTEIN STRUCTURE, TERTIARY; PROTEINS; RNA SPLICE SITES; RNA, MESSENGER; SEQUENCE ALIGNMENT;

EID: 34548245376     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-259     Document Type: Article

References (46)

1. Kriventseva EV, Koch I, Apweiler R, Vingron M, Bork P, Gelfand MS, Sunyaev S: Increase of functional diversity by alternative splicing. Trends Genet 2003, 19(3):124-128.
2. Modrek B, Lee CJ: Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/ or loss. Nat Genet 2003, 34(2):177-180.
3. Xing Y, Lee CJ: Negative selection pressure against premature protein truncation is reduced by alternative splicing and diploidy. Trends Genet 2004, 20(10):472-475.
4. Wen F, Li F, Xia H, Lu X, Zhang X, Li Y: The impact of very short alternative splicing on protein structures and functions in the human genome. Trends Genet 2004, 20(5):232-236.
5. Iida K, Akashi H: A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes. Gene 2000, 261(1):93-105.
6. Hurst LD, Pal C: Evidence for purifying selection acting on silent sites in BRCAI. Trends Genet 2001, 17(2):62-65.
7. Filip LC, Mundy NI: Rapid evolution by positive Darwinian selection in the extracellular domain of the abundant lymphocyte protein CD45 in primates. Mol Biol Evol 2004, 21(8):1504-1511.
8. Ohler U, Shomron N, Burge CB: Recognition of unknown conserved alternatively spliced exons. PLoS Comput Biol 2005, 1(2):113-122.
9. Xing Y, Lee C: Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci U S A 2005, 102(38):13526-13531.
10. Xing Y, Lee C: Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics 2005.
11. Chen FC, Wang SS, Chen CJ, Li WH, Chuang TJ: Alternatively and Constitutively Spliced Exons are Subject to Different Evolutionary Forces. Mol Biol Evol 2005.
12. Nekrutenko A, Makova KD, Li WH: The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study. Genome Res 2002, 12(1):198-202.
13. Nekrutenko A, Chung WY, Li WH: An evolutionary approach reveals a high protein-coding capacity of the human genome. Trends Genet 2003, 19(6):306-310.
14. Berget SM: Exon recognition in vertebrate splicing. J Biol Chem 1995, 270(6):2411-2414.
15. Thanaraj TA, Stamm S: Prediction and statistical analysis of alternatively spliced exons. Prog Mol Subcell Biol 2003, 31:1-31.
16. Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, Shamir R: A non-EST-based method for exon-skipping prediction. Genome Res 2004, 14(8):1617-1623.
17. Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB: Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci U S A 2005, 102(8):2850-2855.
18. Cartegni L, Chew SL, Krainer AR: Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 2002, 3(4):285-298.
19. Xing Y, Xu Q, Lee C: Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains. FEBS Lett 2003, 555(3):572-578.
20. Cline MS, Shigeta R, Wheeler RL, Siani-Rose MA, Kulp D, Loraine AE: The effects of alternative splicing on transmembrane proteins in the mouse genome. Pac Symp Biocomput 2004:17-28.
21. Yeo G, Holste D, Kreiman G, Burge CB: Variation in alternative splicing across human tissues. Genome Biol 2004, 5(10):R74.
22. Wang Z, Rolish ME, Yeo G, Tung V, Mawson M, Burge CB: Systematic identification and analysis of exonic splicing silencers. Cell 2004, 119(6):831-845.
23. Karnaugh M: The Map Method for Synthesis of Combinational Logic Circuits. Trans AIEE pt 1 1953, 72(9):593-599.
24. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R: InterProScan: protein domains identifier. Nucleic Acids Res 2005, 33(Web Server issue):W116-20.
25. Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, Copley R, Courcelle E, Das U, Durbin R, Fleischmann W, Gough J, Haft D, Harte N, Hulo N, Kahn D, Kanapin A, Krestyaninova M, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McDowall J, Mitchell A, Nikolskaya AN, Orchard S, Pagni M, Ponting CP, Quevillon E, Selengut J, Sigrist CJ, Silventoinen V, Studholme DJ, Vaughan R, Wu CH: InterPro, progress and status in 2005. Nucleic Acids Res 2005, 33(Database issue):D201-5.
26. InterProScan package [http://www.ebi.ac.uk/InterProScan/index.html].
27. INTERPRO resource [ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/].
28. Cartegni L, Wang J, Zhu Z, Zhang MQ, Krainer AR: ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Res 2003, 31(13):3568-3571.
29. Fairbrother WG, Yeh RF, Sharp PA, Burge CB: Predictive identification of exonic splicing enhancers in human genes. Science 2002, 297(5583):1007-1013.
30. Fairbrother WG, Yeo GW, Yeh R, Goldstein P, Mawson M, Sharp PA, Burge CB: RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons. Nucleic Acids Res 2004, 32(Web Server issue):W187-90.
31. Fairbrother WG, Holste D, Burge CB, Sharp PA: Single nucleotide polymorphism-based validation of exonic splicing enhancers. PLoS Biol 2004, 2(9):E268.
32. Zhang XH, Chasin LA: Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev 2004, 18(11):1241-1250.
33. Zhang XH, Kangsamaksin T, Chao MS, Banerjee JK, Chasin LA: Exon inclusion is dependent on predictable exonic splicing enhancers. Mol Cell Biol 2005, 25(16):7323-7332.
34. Wang J, Smith PJ, Krainer AR, Zhang MQ: Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res 2005, 33(16):5053-5062.
35. Sorek R, Ast G: Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res 2003, 13(7):1631-1637.
36. Philipps DL, Park JW, Graveley BR: A computational and experimental approach toward a priori identification of alternatively spliced exons. Rna 2004, 10(12):1838-1844.
37. Stamm S, Riethoven JJ, Le Texier V, Gopalakrishnan C, Kumanduri V, Tang Y, Barbosa-Morais NL, Thanaraj TA: ASD: a bioinformatics resource on alternative splicing. Nucleic Acids Res 2006, 34(Database issue):D46-55.
38. Chen FC, Wang SS, Chen CJ, Li WH, Chuang TJ: Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol Biol Evol 2006, 23(3):675-682.
39. Lee C, Atanelov L, Modrek B, Xing Y: ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res 2003, 31(1):101-105.
40. The ASAP database [http://www.bioinformatics.ucla.edu/ASAP/].
41. The UniGene EST sequences [ftp://ftp.ncbi.nih.gov/repository/UniGene/].
42. The ASD database [http://www.ebi.ac.uk/asd/].
43. Sequences analyzed in this study [http://www.sinica.edu.tw/~trees/ ASE_Evolution/ASE_Evolution.htm].
44. Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13(5):555-556.
45. Yang Z, Nielsen R: Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 2000, 17(1):32-43.
46. The R statistics system [http://www.r-project.org/].