Feature-based classification of amino acid substitutions outside conserved functional protein domains

The Scientific World Journal

Volumn 2013, Issue , 2013, Pages

  Gemovic, Branislava ^a   Perovic, Vladimir ^a   Glisic, Sanja ^a   Veljkovic, Nevena ^a  

^a UNIVERSITY OF BELGRADE   (Serbia)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ARGININE; ASPARAGINE; ASPARTIC ACID; ASXL1 PROTEIN; CYSTEINE; DNA METHYLTRANSFERASE 3A; GLUTAMIC ACID; GLUTAMINE; GLYCINE; HISTIDINE; ISOLEUCINE; LEUCINE; LYSINE; MEMBRANE PROTEIN; METHIONINE; PHENYLALANINE; PROLINE; SERINE; TET2 PROTEIN; THREONINE; TRANSCRIPTION FACTOR EZH2; TRYPTOPHAN; TYROSINE; UNCLASSIFIED DRUG; VALINE; ASXL1 PROTEIN, HUMAN; DNA (CYTOSINE 5) METHYLTRANSFERASE; DNA BINDING PROTEIN; EZH2 PROTEIN, HUMAN; ONCOPROTEIN; POLYCOMB REPRESSIVE COMPLEX 2; PROTEIN; REPRESSOR PROTEIN; TET2 PROTEIN, HUMAN;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOTRANSFORMATION; CLASSIFICATION; GENETIC POLYMORPHISM; LYMPHOMA; MISSENSE MUTATION; MUTATIONAL ANALYSIS; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FUNCTION; SEQUENCE HOMOLOGY; WILD TYPE; BIOLOGY; CHEMISTRY; GENETIC DATABASE; GENETIC EPIGENESIS; GENETICS; HUMAN; METABOLISM; METHODOLOGY; RECEIVER OPERATING CHARACTERISTIC;

ALGORITHMS; AMINO ACID SUBSTITUTION; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA-BINDING PROTEINS; EPIGENESIS, GENETIC; HUMANS; POLYCOMB REPRESSIVE COMPLEX 2; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS; PROTO-ONCOGENE PROTEINS; REPRESSOR PROTEINS; ROC CURVE;

EID: 84890056814     PISSN: None     EISSN: 1537744X     Source Type: Journal    
DOI: 10.1155/2013/948617     Document Type: Article

References (58)

1. Abecasis G. R., Auton A., Brooks L. D., An integrated map of genetic variation from 1,092 human genomes. Nature 2012 491 7422 56 65 10.1038/nature11632
2. Harrow J., Frankish A., Gonzalez J. M., GENCODE: the reference human genome annotation for the ENCODE Project. Genome Research 2012 22 9 1760 1774 10.1101/gr.135350.111
3. Abecasis G. R., Altshuler D., Auton A., A map of human genome variation from population-scale sequencing. Nature 2010 467 7319 1061 1073 10.1038/nature09534
4. Tennessen J. A., Bigham A. W., O'Connor T. D., Evolution and functional impact of rare coding variation from deep sequencing of human exomes. Science 2012 337 6090 64 69
5. Gonzalez de Castro D., Clarke P. A., Al-Lazikani B., Workman P., Personalized cancer medicine: molecular diagnostics, predictive biomarkers, and drug resistance. Clinical Pharmacology and Therapeutics 2013 93 3 252 259 10.1038/clpt.2012.237
6. Jordan D. M., Ramensky V. E., Sunyaev S. R., Human allelic variation: perspective from protein function, structure, and evolution. Current Opinion in Structural Biology 2010 20 3 342 350 2-s2.0-77955590137 10.1016/j.sbi.2010.03. 006
7. Wu J., Jiang R., Prediction of deleterious nonsynonymous single-nucleotide polymorphism for human diseases. The Scientific World Journal 2013 2013 10 10.1155/2013/675851 675851
8. Thomas P. D., Campbell M. J., Kejariwal A., Mi H., Karlak B., Daverman R., Diemer K., Muruganujan A., Narechania A., PANTHER: a library of protein families and subfamilies indexed by function. Genome Research 2003 13 9 2129 2141 2-s2.0-0141742293 10.1101/gr.772403 (Pubitemid 37161770)
9. 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 2-s2.0-33751013750 10.1093/bioinformatics/btl423 (Pubitemid 44742391)
10. Ng P. C., Henikoff S., Predicting deleterious amino acid substitutions. Genome Research 2001 11 5 863 874 2-s2.0-0035026704 10.1101/gr.176601 (Pubitemid 32447869)
11. Li B., Krishnan V. G., Mort M. E., Xin F., Kamati K. K., Cooper D. N., Mooney S. D., Radivojac P., Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics 2009 25 21 2744 2750 2-s2.0-70350671733 10.1093/bioinformatics/btp528
12. Bromberg Y., Rost B., SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Research 2007 35 11 3823 3835 2-s2.0-34547100092 10.1093/nar/gkm238 (Pubitemid 47244674)
13. Adzhubei I. A., Schmidt S., Peshkin L., Ramensky V. E., Gerasimova A., Bork P., Kondrashov A. S., Sunyaev S. R., A method and server for predicting damaging missense mutations. Nature Methods 2010 7 4 248 249 2-s2.0-77951640946 10.1038/nmeth0410-248
14. Luo H., Nijveen H., Understanding and identifying amino acid repeats. Briefings in Bioinformatics 2013 10.1093/bib/bbt003
15. Shen H.-B., Chou K.-C., PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition. Analytical Biochemistry 2008 373 2 386 388 2-s2.0-37549004451 10.1016/j.ab.2007.10.012
16. Veljkovic V., Veljkovic N., Esté J. A., Hüther A., Dietrich U., Application of the EIIP/ISM bioinformatics concept in development of new drugs. Current Medicinal Chemistry 2007 14 4 441 453 2-s2.0-33847215785 10.2174/092986707779941014
17. Glisic S., Arrigo P., Alavantic D., Perovic V., Prljic J., Veljkovic N., Lipoprotein lipase: a bioinformatics criterion for assessment of mutations as a risk factor for cardiovascular disease. Proteins: Structure, Function and Genetics 2008 70 3 855 862 2-s2.0-38549089000 10.1002/prot.21581 (Pubitemid 351161944)
18. Hu W., Quantifying the effects of mutations on receptor binding specificity of influenza viruses. Journal of Biomedical Science and Engineering 2010 3 3 227 240 10.4236/jbise.2010.33031
19. Nwankwo N., Seker H., A signal processing-based Bioinformatics approach to assessing drug resistance: human Immunodeficiency Virus as a case study. Proceedings of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '10) September 2010 Buenos Aires, Argentina 1836 1839 2-s2.0-78650817470 10.1109/IEMBS.2010.5626439
20. Perovic V. R., Muller C. P., Niman H. L., Novel phylogenetic algorithm to monitor human tropism in Egyptian H5N1-HPAIV reveals evolution toward efficient human-to-human transmission. PLoS ONE 2013 8 4 e61572
21. Mancini M., Veljkovic N., Leo E., Cytoplasmatic compartmentalization by Bcr-Abl promotes TET2 loss-of-function in chronic myeloid leukemia. Journal of Cellular Biochemistry 2012 113 8 2765 2774 10.1002/jcb.24154
22. Kumar S., Dudley J. T., Filipski A., Liu L., Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations. Trends in Genetics 2011 27 9 377 386 2-s2.0-84856613697
23. Yue P., Forrest W. F., Kaminker J. S., Lohr S., Zhang Z., Cavet G., Inferring the functional effects of mutation through clusters of mutations in homologous proteins. Human Mutation 2010 31 3 264 271 2-s2.0-77149124860 10.1002/humu.21194
24. Sant M., Allemani C., Tereanu C., Incidence of hematologic malignancies in Europe by morphologic subtype: results of the HAEMACARE project. Blood 2010 116 19 3724 3734 10.1182/blood-2010-05-282632
25. Bejar R., Stevenson K., Abdel-Wahab O., Galili N., Nilsson B., Garcia-Manero G., Kantarjian H., Raza A., Levine R. L., Neuberg D., Ebert B. L., Clinical effect of point mutations in myelodysplastic syndromes. The New England Journal of Medicine 2011 364 26 2496 2506 2-s2.0-79959794787 10.1056/NEJMoa1013343
26. Grossmann V., Kohlmann A., Eder C., Haferlach C., Kern W., Cross N. C. P., Haferlach T., Schnittger S., Molecular profiling of chronic myelomonocytic leukemia reveals diverse mutations in >80% of patients with TET2 and EZH2 being of high prognostic relevance. Leukemia 2011 25 5 877 879 2-s2.0-79955810336 10.1038/leu.2011.10
27. Guglielmelli P., Biamonte F., Score J., Hidalgo-Curtis C., Cervantes F., Maffioli M., Fanelli T., Ernst T., Winkelman N., Jones A. V., Zoi K., Reiter A., Duncombe A., Villani L., Bosi A., Barosi G., Cross N. C. P., Vannucchi A. M., EZH2 mutational status predicts poor survival in myelofibrosis. Blood 2011 118 19 5227 5234 2-s2.0-81055126771 10.1182/blood-2011-06-363424
28. Metzeler K. H., Maharry K., Radmacher M. D., Mrózek K., Margeson D., Becker H., Curfman J., Holland K. B., Schwind S., Whitman S. P., Wu Y.-Z., Blum W., Powell B. L., Carter T. H., Wetzler M., Moore J. O., Kolitz J. E., Baer M. R., Carroll A. J., Larson R. A., Caligiuri M. A., Marcucci G., Bloomfield C. D., TET2 mutations improve the new European LeukemiaNet risk classification of acute myeloid leukemia: a cancer and leukemia group B study. Journal of Clinical Oncology 2011 29 10 1373 1381 2-s2.0-79954428737 10.1200/JCO.2010.32.7742
29. Metzeler K. H., Becker H., Maharry K., Radmacher M. D., Kohlschmidt J., Mrózek K., Nicolet D., Whitman S. P., Wu Y.-Z., Schwind S., Powell B. L., Carter T. H., Wetzler M., Moore J. O., Kolitz J. E., Baer M. R., Carroll A. J., Larson R. A., Caligiuri M. A., Marcucci G., Bloomfield C. D., ASXL1 mutations identify a high-risk subgroup of older patients with primary cytogenetically normal AML within the ELN Favorable genetic category. Blood 2011 118 26 6920 6929 2-s2.0-84255176496 10.1182/blood-2011-08-368225
30. Thol F., Friesen I., Damm F., Yun H., Weissinger E. M., Krauter J., Wagner K., Chaturvedi A., Sharma A., Wichmann M., Göhring G., Schumann C., Bug G., Ottmann O., Hofmann W.-K., Schlegelberger B., Heuser M., Ganser A., Prognostic significance of ASXL1 mutations in patients with myelodysplastic syndromes. Journal of Clinical Oncology 2011 29 18 2499 2506 2-s2.0-79959317767 10.1200/JCO.2010.33.4938
31. Walter M. J., Ding L., Shen D., Shao J., Grillot M., McLellan M., Fulton R., Schmidt H., Kalicki-Veizer J., O'Laughlin M., Kandoth C., Baty J., Westervelt P., Dipersio J. F., Mardis E. R., Wilson R. K., Ley T. J., Graubert T. A., Recurrent DNMT3A mutations in patients with myelodysplastic syndromes. Leukemia 2011 25 7 1153 1158 2-s2.0-79960255863 10.1038/leu.2011.44
32. Gelsi-Boyer V., Brecqueville M., Devillier R., Murati A., Mozziconacci M.-J., Birnbaum D., Mutations in ASXL1 are associated with poor prognosis across the spectrum of malignant myeloid diseases. Journal of Hematology & Oncology 2012 5, article 12 6 2-s2.0-84858600403 10.1186/1756-8722-5-12
33. Tahiliani M., Koh K. P., Shen Y., Pastor W. A., Bandukwala H., Brudno Y., Agarwal S., Iyer L. M., Liu D. R., Aravind L., Rao A., Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 2009 324 5929 930 935 2-s2.0-66149146320 10.1126/science.1170116
34. Okano M., Bell D. W., Haber D. A., Li E., DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 1999 99 3 247 257 2-s2.0-0033615717 10.1016/S0092-8674(00)81656-6 (Pubitemid 29519904)
35. Kuzmichev A., Nishioka K., Erdjument-Bromage H., Tempst P., Reinberg D., Histone methyltransferase activity associated with a human multiprotein complex containing the enhancer of zeste protein. Genes and Development 2002 16 22 2893 2905 2-s2.0-0037111831 10.1101/gad.1035902 (Pubitemid 35334738)
36. Brock H. W., Fisher C. L., Maintenance of gene expression patterns. Developmental Dynamics 2005 232 3 633 655 2-s2.0-14644392179 10.1002/dvdy.20298 (Pubitemid 40315285)
37. Shih A. H., Abdel-Wahab O., Patel J. P., Levine R. L., The role of mutations in epigenetic regulators in myeloid malignancies. Nature Reviews: Cancer 2012 12 9 599 612
38. Jankowska A. M., Makishima H., Tiu R. V., Szpurka H., Huang Y., Traina F., Visconte V., Sugimoto Y., Prince C., O'Keefe C., Hsi E. D., List A., Sekeres M. A., Rao A., McDevitt M. A., Maciejewski J. P., Mutational spectrum analysis of chronic myelomonocytic leukemia includes genes associated with epigenetic regulation: UTX, EZH2, and DNMT3A. Blood 2011 118 14 3932 3941 2-s2.0-80053135096 10.1182/blood-2010-10-311019
39. Langemeijer S. M. C., Kuiper R. P., Berends M., Knops R., Aslanyan M. G., Massop M., Stevens-Linders E., Van Hoogen P., Van Kessel A. G., Raymakers R. A. P., Kamping E. J., Verhoef G. E., Verburgh E., Hagemeijer A., Vandenberghe P., De Witte T., Van Der Reijden B. A., Jansen J. H., Acquired mutations in TET2 are common in myelodysplastic syndromes. Nature Genetics 2009 41 7 838 842 2-s2.0-67649876132 10.1038/ng.391
40. UniProt Consortium, Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Research 2013 41 D1 D43 D47 10.1093/nar/gks1068
41. Forbes S. A., Bindal N., Bamford S., Cole C., Kok C. Y., Beare D., Jia M., Shepherd R., Leung K., Menzies A., Teague J. W., Campbell P. J., Stratton M. R., Futreal P. A., COSMIC: mining complete cancer genomes in the catalogue of somatic mutations in cancer. Nucleic Acids Research 2011 39 1 D945 D950 2-s2.0-78651330430 10.1093/nar/gkq929
42. Veljković V., Slavić I., Simple general-model pseudopotential. Physical Review Letters 1972 29 2 105 107 2-s2.0-35949031045 10.1103/PhysRevLett.29.105
43. Gruber M., Söding J., Lupas A. N., REPPER-repeats and their periodicities in fibrous proteins. Nucleic Acids Research 2005 33 2 W239 W243 2-s2.0-23144450570 10.1093/nar/gki405 (Pubitemid 44529916)
44. Marsella L., Sirocco F., Trovato A., Seno F., Tosatto S. C. E., REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform. Bioinformatics 2009 25 12 i289 i295 2-s2.0-66349088076 10.1093/bioinformatics/btp232
45. Morin R. D., Johnson N. A., Severson T. M., Mungall A. J., An J., Goya R., Paul J. E., Boyle M., Woolcock B. W., Kuchenbauer F., Yap D., Humphries R. K., Griffith O. L., Shah S., Zhu H., Kimbara M., Shashkin P., Charlot J. F., Tcherpakov M., Corbett R., Tam A., Varhol R., Smailus D., Moksa M., Zhao Y., Delaney A., Qian H., Birol I., Schein J., Moore R., Holt R., Horsman D. E., Connors J. M., Jones S., Aparicio S., Hirst M., Gascoyne R. D., Marra M. A., Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nature Genetics 2010 42 2 181 185 2-s2.0-75749124332 10.1038/ng.518
46. Punta M., Coggill P. C., Eberhardt R. Y., The Pfam protein families database. Nucleic Acids Research 2012 40 D1 D290 D301 10.1093/nar/gkr1065
47. Hicks S., Wheeler D. A., Plon S. E., Kimmel M., Prediction of missense mutation functionality depends on both the algorithm and sequence alignment employed. Human Mutation 2011 32 6 661 668 2-s2.0-79957621519 10.1002/humu.21490
48. Veljkovic N., Glisic S., Prljic J., Perovic V., Botta M., Veljkovic V., Discovery of new therapeutic targets by the informational spectrum method. Current Protein and Peptide Science 2008 9 5 493 506 2-s2.0-55949129355 10.2174/138920308785915245
49. Jonsson P. F., Bates P. A., Global topological features of cancer proteins in the human interactome. Bioinformatics 2006 22 18 2291 2297 2-s2.0-33748706765 10.1093/bioinformatics/btl390 (Pubitemid 44390886)
50. Mintseris J., Weng Z., Structure, function, and evolution of transient and obligate protein-protein interactions. Proceedings of the National Academy of Sciences of the United States of America 2005 102 31 10930 10935 2-s2.0-23344451687 10.1073/pnas.0502667102 (Pubitemid 41105970)
51. Vardiman J. W., The World Health Organization (WHO) classification of tumors of the hematopoietic and lymphoid tissues: an overview with emphasis on the myeloid neoplasms. Chemico-Biological Interactions 2010 184 1-2 16 20 2-s2.0-77950624688 10.1016/j.cbi.2009.10.009
52. Tokuriki N., Tawfik D. S., Stability effects of mutations and protein evolvability. Current Opinion in Structural Biology 2009 19 5 596 604 2-s2.0-70349901079 10.1016/j.sbi.2009.08.003
53. Yue P., Li Z., Moult J., Loss of protein structure stability as a major causative factor in monogenic disease. Journal of Molecular Biology 2005 353 2 459 473 2-s2.0-25144523127 10.1016/j.jmb.2005.08.020 (Pubitemid 41356624)
54. González-Pérez A., López-Bigas N., Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. American Journal of Human Genetics 2011 88 4 440 449 2-s2.0-79953715693 10.1016/j.ajhg.2011.03.004
55. Li M. X., Kwan J. S., Bao S. Y., Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies. PLoS Genetics 2013 9 1 10.1371/journal.pgen.1003143 e1003143
56. Schymkowitz J., Borg J., Stricher F., Nys R., Rousseau F., Serrano L., The FoldX web server: an online force field. Nucleic Acids Research 2005 33 supplement 2 W382 W388 10.1093/nar/gki387 (Pubitemid 44529948)
57. Parthiban V., Gromiha M. M., Schomburg D., CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Research 2006 34 supplement 2 W239 W242 10.1093/nar/gkl190 (Pubitemid 44529771)
58. Yin S., Ding F., Dokholyan N. V., Eris: an automated estimator of protein stability. Nature Methods 2007 4 6 466 746 10.1038/nmeth0607-466 (Pubitemid 46852064)