메뉴 건너뛰기




Volumn 1, Issue 3, 2009, Pages 220-228

Computational and structural analysis of deleterious functional SNPs in ARNT oncogene

Author keywords

acute myeloblastic leukemia; ARNT gene; mutations; PolyPhen

Indexed keywords

AMINO ACID; ARNT PROTEIN, HUMAN; HYPOXIA INDUCIBLE FACTOR 1BETA;

EID: 77956629568     PISSN: 19132751     EISSN: 18671462     Source Type: Journal    
DOI: 10.1007/s12539-009-0042-9     Document Type: Article
Times cited : (5)

References (48)
  • 1
    • 0037183788 scopus 로고    scopus 로고
    • A CH⋯O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins
    • Babu, M. M., Singh, K. S., Balaram, P. 2002. A CH⋯O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins. J Mol Biol 322, 871-880.
    • (2002) J Mol Biol , vol.322 , pp. 871-880
    • Babu, M.M.1    Singh, K.S.2    Balaram, P.3
  • 3
    • 3142695439 scopus 로고    scopus 로고
    • Germline Ecadherin mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic screening criteria
    • Brooks-Wilson, A. R., Kaurah, P., Suriano, G. 2004. Germline Ecadherin mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic screening criteria. J Med Genet 41, 508-517.
    • (2004) J Med Genet , vol.41 , pp. 508-517
    • Brooks-Wilson, A.R.1    Kaurah, P.2    Suriano, G.3
  • 4
    • 0036544654 scopus 로고    scopus 로고
    • Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1
    • Cartegni, L., Krainer, A. R. 2002. Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nature Genet 30, 377-384.
    • (2002) Nature Genet , vol.30 , pp. 377-384
    • Cartegni, L.1    Krainer, A.R.2
  • 5
    • 0025150383 scopus 로고
    • Origins of structure in globular proteins
    • Chan, H. S., Dill, K. A. 1990. Origins of structure in globular proteins. Proc Natl Acad Sci 87, 6388-6392.
    • (1990) Proc Natl Acad Sci , vol.87 , pp. 6388-6392
    • Chan, H.S.1    Dill, K.A.2
  • 6
    • 20144377620 scopus 로고    scopus 로고
    • Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
    • Chen, H., Zhou, H. X. 2005. Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res 33, 3193-3199.
    • (2005) Nucleic Acids Res , vol.33 , pp. 3193-3199
    • Chen, H.1    Zhou, H.X.2
  • 7
    • 0035819469 scopus 로고    scopus 로고
    • Toward Mechanism-Based Cancer Care
    • David, M., Livingston, Shivdasani, R. 2001. Toward Mechanism-Based Cancer Care. JAMA 285, 588-593.
    • (2001) Jama , vol.285 , pp. 588-593
    • David, M.1    Livingston, R.2    Shivdasani, R.3
  • 8
    • 2342518038 scopus 로고    scopus 로고
    • On the use of lowfrequency normal modes to enforce collective movements in refining macromolecular structural models
    • Delarue, M., Dumas, P. 2004. On the use of lowfrequency normal modes to enforce collective movements in refining macromolecular structural models. Proc Natl Acad Sci 101, 6957-6962.
    • (2004) Proc Natl Acad Sci , vol.101 , pp. 6957-6962
    • Delarue, M.1    Dumas, P.2
  • 9
    • 0025043276 scopus 로고
    • Mutations within the rhodopsin gene in patients with autosomal dominant retinitis Pigmentosa
    • Dryja, T. P., McGee, T. L., Hahn, L. B., Cowley, G. S., Olsson, J. E., Reichel, E. 1990. Mutations within the rhodopsin gene in patients with autosomal dominant retinitis Pigmentosa. N Engl J Med 323, 1302-1307.
    • (1990) N Engl J Med , vol.323 , pp. 1302-1307
    • Dryja, T.P.1    McGee, T.L.2    Hahn, L.B.3    Cowley, G.S.4    Olsson, J.E.5    Reichel, E.6
  • 10
    • 1842788912 scopus 로고    scopus 로고
    • Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins
    • Eyal, E., Najmanovich, R., Brendan, J., McConkey, Edelman, Sobolev, V. 2004. Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. J Comput Chem 25, 712-724.
    • (2004) J Comput Chem , vol.25 , pp. 712-724
    • Eyal, E.1    Najmanovich, R.2    Brendan, J.3    McConkey, E.4    Sobolev, V.5
  • 12
    • 0029873155 scopus 로고    scopus 로고
    • Stability changes upon mutation of solvent accessible residues in proteins evaluated by database derived potentials
    • Gilis, D., Rooman, M. 1996. Stability changes upon mutation of solvent accessible residues in proteins evaluated by database derived potentials. J Mol Biol 257, 1112-1126.
    • (1996) J Mol Biol , vol.257 , pp. 1112-1126
    • Gilis, D.1    Rooman, M.2
  • 13
    • 0030777760 scopus 로고    scopus 로고
    • Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence
    • Gilis, D., Rooman, M. 1997. Predicting protein stability changes upon mutation using database-derived potentials: solvent accessibility determines the importance of local versus non-local interactions along the sequence. J Mol Biol 272, 276-290.
    • (1997) J Mol Biol , vol.272 , pp. 276-290
    • Gilis, D.1    Rooman, M.2
  • 14
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogenbonded and geometrical features
    • Kabsch, W., Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogenbonded and geometrical features. Biopolymers 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 17
    • 33747858757 scopus 로고    scopus 로고
    • NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
    • Lindahl, E., Azuara, C., Koehl, P., Delarue, M. 2006. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res 34, W52-W56.
    • (2006) Nucleic Acids Res , vol.34
    • Lindahl, E.1    Azuara, C.2    Koehl, P.3    Delarue, M.4
  • 20
    • 18544364500 scopus 로고    scopus 로고
    • Screening for Deleterious non-synonymous Single-Nucleotide Polymorphisms in Genes Involved in Steroid Hormone Metabolism and Response
    • Johnson, M. M., Houck, J., Chu, C. 2005. Screening for Deleterious non-synonymous Single-Nucleotide Polymorphisms in Genes Involved in Steroid Hormone Metabolism and Response. Cancer Epidemiol Biomarkers Prev 14, 1326-1329.
    • (2005) Cancer Epidemiol Biomarkers Prev , vol.14 , pp. 1326-1329
    • Johnson, M.M.1    Houck, J.2    Chu, C.3
  • 21
    • 0035026704 scopus 로고    scopus 로고
    • Predicting Deleterious Amino Acid Substitutions
    • Ng, P. C., Henikoff, S. 2001. Predicting Deleterious Amino Acid Substitutions. Genome Res 11, 863-874.
    • (2001) Genome Res , vol.11 , pp. 863-874
    • Ng, P.C.1    Henikoff, S.2
  • 22
    • 0036119504 scopus 로고    scopus 로고
    • Accounting for Human polymorphisms predicted to affect protein
    • Ng, P. C., Henikoff, S. 2002. Accounting for Human polymorphisms predicted to affect protein. Genome Res 12, 436-446.
    • (2002) Genome Res , vol.12 , pp. 436-446
    • Ng, P.C.1    Henikoff, S.2
  • 23
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: predicting amino acid changes that affect protein Function
    • Ng, P. C., Henikoff, S. 2003. SIFT: predicting amino acid changes that affect protein Function. Nucl Acids Res 31, 3812-3814.
    • (2003) Nucl Acids Res , vol.31 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 24
    • 0028296185 scopus 로고
    • Mining treasures from 'junk DNA
    • Nowak, R. 1994. Mining treasures from 'junk DNA'. Science 263, 608-610.
    • (1994) Science , vol.263 , pp. 608-610
    • Nowak, R.1
  • 25
    • 0033198381 scopus 로고    scopus 로고
    • Internet resources for the functional analysis of 5′ and 3′ untranslated regions of eukaryotic mRNA
    • Pesole, G., Liuni, S. 1999. Internet resources for the functional analysis of 5′ and 3′ untranslated regions of eukaryotic mRNA. TIG 15, 378.
    • (1999) Tig , vol.15 , pp. 378
    • Pesole, G.1    Liuni, S.2
  • 26
    • 0036087522 scopus 로고    scopus 로고
    • UTRdb and UTRsite: specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs
    • Pesole, G., Liuni, S., Grillo, S., Licciulli, F., Mignone, F., Gissi, C., Saccone, C. 2002. UTRdb and UTRsite: specialized databases of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Nucleic Acids Research 30, 335-340.
    • (2002) Nucleic Acids Research , vol.30 , pp. 335-340
    • Pesole, G.1    Liuni, S.2    Grillo, S.3    Licciulli, F.4    Mignone, F.5    Gissi, C.6    Saccone, C.7
  • 27
    • 0020407278 scopus 로고
    • Synthesis of betahexosaminidase in cell-free translation and in intact fibroblasts: an insoluble precursor alpha chain in a rare form of Tay Sachs disease
    • Proia, R. L., Neufeld, E. F. 1982. Synthesis of betahexosaminidase in cell-free translation and in intact fibroblasts: an insoluble precursor alpha chain in a rare form of Tay Sachs disease. Proc Natl Acad Sci 79, 6360-6364.
    • (1982) Proc Natl Acad Sci , vol.79 , pp. 6360-6364
    • Proia, R.L.1    Neufeld, E.F.2
  • 28
    • 18844366475 scopus 로고    scopus 로고
    • Regulatory SNPs in complex diseases: their identification and functional validation
    • Prokunina, L., Alarcon-Riquelme, M. E. 2004. Regulatory SNPs in complex diseases: their identification and functional validation. Expert Rev Mol Med 6, 1-15.
    • (2004) Expert Rev Mol Med , vol.6 , pp. 1-15
    • Prokunina, L.1    Alarcon-Riquelme, M.E.2
  • 29
  • 30
    • 3442879338 scopus 로고    scopus 로고
    • Assessing the function of genetic variants in candidate gene association studies
    • Rebbeck, T. R., Spitz, M., Wu, X. 2004. Assessing the function of genetic variants in candidate gene association studies. Nat Rev Genet 5, 589-597.
    • (2004) Nat Rev Genet , vol.5 , pp. 589-597
    • Rebbeck, T.R.1    Spitz, M.2    Wu, X.3
  • 31
    • 33745862379 scopus 로고    scopus 로고
    • Predicting deleterious nsSNPs: an analysis of sequence and structural attributes
    • Richard, J. D., Patricia, B. M., Mark, J. C., Mansoor, Saqi, A. S. 2006. Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. BMC Bioinformatics 7, 217.
    • (2006) BMC Bioinformatics , vol.7 , pp. 217
    • Richard, J.D.1    Patricia, B.M.2    Mark, J.C.3    Mansoor4    Saqi, A.S.5
  • 32
    • 0037438384 scopus 로고    scopus 로고
    • Stability of cyclic beta-hairpins: asymmetric contributions from side chains of a hydrogen-bonded cross-strand residue pair
    • Russell, S. J., Blandl, T., Skelton, N. J., Cochran, A. G. 2003. Stability of cyclic beta-hairpins: asymmetric contributions from side chains of a hydrogen-bonded cross-strand residue pair. J Am Chem Soc 125, 388-395.
    • (2003) J Am Chem Soc , vol.125 , pp. 388-395
    • Russell, S.J.1    Blandl, T.2    Skelton, N.J.3    Cochran, A.G.4
  • 34
    • 2942604293 scopus 로고    scopus 로고
    • Identifying functional genetic variants in DNA repair pathway using protein conservation analysis
    • Savas, S., Kim, D. Y., Ahmad, M. F., Shariff, M., Ozcelik, H. 2004. Identifying functional genetic variants in DNA repair pathway using protein conservation analysis. Cancer Epidemiol Biomarkers Prev 13, 801-807.
    • (2004) Cancer Epidemiol Biomarkers Prev , vol.13 , pp. 801-807
    • Savas, S.1    Kim, D.Y.2    Ahmad, M.F.3    Shariff, M.4    Ozcelik, H.5
  • 35
    • 37949017674 scopus 로고    scopus 로고
    • ASA view: solvent accessibility graphics for proteins
    • Shander, A., Gromiha, M., Fawareh, H., Sarai, A. 2004. ASA view: solvent accessibility graphics for proteins. Bioinformatics 51, 51.
    • (2004) Bioinformatics , vol.51 , pp. 51
    • Shander, A.1    Gromiha, M.2    Fawareh, H.3    Sarai, A.4
  • 38
    • 0034191958 scopus 로고    scopus 로고
    • Towards a structural basis of human nonsynonymous single nucleotide polymorphisms
    • Sunyaev, S., Ramensky, V., Bork, P. 2000. Towards a structural basis of human nonsynonymous single nucleotide polymorphisms. Trends Genet 16, 198-200.
    • (2000) Trends Genet , vol.16 , pp. 198-200
    • Sunyaev, S.1    Ramensky, V.2    Bork, P.3
  • 40
    • 0028266931 scopus 로고
    • mRNA translation: influence of the 5′ and 3′ untranslated Regions
    • Sonenberg, N. 1994. mRNA translation: influence of the 5′ and 3′ untranslated Regions. Curr Opin Genet 4, 310-315.
    • (1994) Curr Opin Genet , vol.4 , pp. 310-315
    • Sonenberg, N.1
  • 41
    • 42449139081 scopus 로고    scopus 로고
    • Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis
    • Swapan, K. D., Neeraj, K. S., Winston, S. C., Hua, W., Steven, C. E. 2008. Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis. BMC Medical Genetics 9, 16.
    • (2008) BMC Medical Genetics , vol.9 , pp. 16
    • Swapan, K.D.1    Neeraj, K.S.2    Winston, S.C.3    Hua, W.4    Steven, C.E.5
  • 42
    • 0033365404 scopus 로고    scopus 로고
    • Identification of mutations in the repeated part of the autosomal dominant polycystic kidney disease type 1 gene PKD1, by long-range PCR
    • Thomas, R., McConnell, R., Whittacker, J., Kirkpatrick, P., Bradley, J., Sandford, R. 1999. Identification of mutations in the repeated part of the autosomal dominant polycystic kidney disease type 1 gene PKD1, by long-range PCR. Am J Hum Genet 65, 39-49.
    • (1999) Am J Hum Genet , vol.65 , pp. 39-49
    • Thomas, R.1    McConnell, R.2    Whittacker, J.3    Kirkpatrick, P.4    Bradley, J.5    Sandford, R.6
  • 43
    • 1442354863 scopus 로고    scopus 로고
    • Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking
    • Totrov, M. 2004. Accurate and efficient generalized born model based on solvent accessibility: derivation and application for LogP octanol/water prediction and flexible peptide docking. J Comput Chem 25, 609-619.
    • (2004) J Comput Chem , vol.25 , pp. 609-619
    • Totrov, M.1
  • 44
    • 0034026082 scopus 로고    scopus 로고
    • Cytokine and cytokine receptor polymorphisms in infectious disease
    • van Deventer, S. 2000. Cytokine and cytokine receptor polymorphisms in infectious disease. Intensive Care Med 26, S98-S102.
    • (2000) Intensive Care Med , vol.26
    • van Deventer, S.1
  • 45
    • 0037093647 scopus 로고    scopus 로고
    • Positioning of anchor groups in protein loop prediction: the importance of solvent accessibility and secondary structure elements
    • Wohlfahrt, G., Hangoc, V. U., Schomburg, D. 2002. Positioning of anchor groups in protein loop prediction: the importance of solvent accessibility and secondary structure elements. Proteins 47, 370-378.
    • (2002) Proteins , vol.47 , pp. 370-378
    • Wohlfahrt, G.1    Hangoc, V.U.2    Schomburg, D.3
  • 46
    • 2642527702 scopus 로고    scopus 로고
    • Many amino acid substitution variants identified in DNA repair genes during human population screenings are predicted to impact protein function
    • Xi, T., Jones, I. M., Mohrenweiser, H. W. 2004. Many amino acid substitution variants identified in DNA repair genes during human population screenings are predicted to impact protein function. Genomics 83, 970-979.
    • (2004) Genomics , vol.83 , pp. 970-979
    • Xi, T.1    Jones, I.M.2    Mohrenweiser, H.W.3
  • 47
    • 0011830097 scopus 로고
    • Molecular abnormality of an inactive aldehyde dehydrogenase variant commonly found in Orientals
    • Yoshida, A., Huang, I. Y., Ikawa, M. 1984. Molecular abnormality of an inactive aldehyde dehydrogenase variant commonly found in Orientals. Proc Natl Acad Sci 81, 258-261.
    • (1984) Proc Natl Acad Sci , vol.81 , pp. 258-261
    • Yoshida, A.1    Huang, I.Y.2    Ikawa, M.3
  • 48
    • 3343020872 scopus 로고    scopus 로고
    • Genetic polymorphisms in human protondependent dipeptide transporter PEPT1: implications for the functional role of Pro586
    • Zhang, E. Y., Fu, D. J., Pak, Y. A., Stewart, T., Mukhopadhyay, N., Wrighton, S. A., Hillgren, K. M. 2004. Genetic polymorphisms in human protondependent dipeptide transporter PEPT1: implications for the functional role of Pro586. J Pharmacol Exp Ther 310, 437-445.
    • (2004) J Pharmacol Exp Ther , vol.310 , pp. 437-445
    • Zhang, E.Y.1    Fu, D.J.2    Pak, Y.A.3    Stewart, T.4    Mukhopadhyay, N.5    Wrighton, S.A.6    Hillgren, K.M.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.