Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches

Bioinformatics

Volumn 22, Issue 7, 2006, Pages 775-778

  Pellegrini Calace, Marialuisa ^a   Tramontano, Anna ^a,b  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b Pasteur Institute   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; MITOGEN ACTIVATED PROTEIN KINASE;

ARTICLE; CHROMOSOME 21; COMPUTER ANALYSIS; DOWN SYNDROME; GENE LOCATION; HUMAN; HUMAN CHROMOSOME; HYPOTHESIS; MENTAL DEFICIENCY; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; STATISTICAL MODEL; TRISOMY 21; VALIDATION PROCESS;

EID: 33645309356     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl006     Document Type: Article

References (36)

1. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Ashburner,M. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
3. Baldus,C.D. et al. (2004) Acute myeloid leukemia with complex karyotypes and abnormal chromosome 21: Amplification discloses overexpression of APP, ETS2, and ERG genes. Proc. Natl Acad. Sci. USA, 101, 3915-3920.
4. Bateman,A. et al. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280.
5. Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
6. Birchler,J.A. et al. (2005) Dosage balance in gene regulation: biological implications. Trends Genet., 21, 219-226.
7. Branchi,I. et al. (2004) Transgenic mouse in vivo library of human Down syndrome critical region 1: Association between DYRK1A overexpression, brain development abnormalities, and cell cycle protein alteration. J. Neuropathol. Exp. Neurol., 63, 429-440.
8. Delabar,J.M. et al. (1993) Molecular mapping of twenty-four features of Down syndrome on chromosome 21. Eur. J. Hum. Genet., 1, 114-124.
9. Eddy,S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
10. Epstein,C.J. et al. (1991) Protocols to establish genotype-phenotype correlations in Down syndrome. Am. J. Hum. Genet., 49, 207-235.
11. Galceran,J. et al. (2003) The MNB/DYRK1A protein kinase: Genetic and biochemical properties. J Neural Transm Suppl., 67, 139-148.
12. Gardiner,K. et al. (2003) Mouse models of Down syndrome: How useful can they be? Comparison of the gene content of human chromosome 21 with orthologous mouse genomic regions. Gene, 318, 137-147.
13. Gardiner,K. et al. (2005) Report on the 'Expert Workshop on the Biology of Chromosome 21: Towards gene-phenotype correlations in Down syndrome', held June 11-14, 2004, Washington D.C. Cytogenet. Genome Res., 108, 269-277.
14. Gurbuxani,S. et al. (2004) Recent insights into the mechanisms of myeloid leukemogenesis in Down syndrome. Blood, 103, 399-406.
15. Haft,C.R. et al. (2000) Human orthologs of yeast vacuolar protein sorting proteins Vps26, 29, and 35: Assembly into multimeric complexes. Mol. Biol. Cell, 11, 4105-4116.
16. Hammerle,B. et al. (2003) Expression patterns and subcellular localization of the Down syndrome candidate protein MNB/DYRK1A suggest a role in late neuronal differentiation. Eur. J. Neurosci., 17, 2277-2286.
17. Hamosh,A. et al. (2005) Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res., 33, D514-D517.
18. Harada,T. et al. (2003) AKRL1 and AKRL2 activate the JNK pathway. Genes Cells, 8, 493-500.
19. Hattori,M. et al. (2000) The DNA sequence of human chromosome 21 [Erratum (2000) Nature, 407, 110.]. Nature, 18, 311-319.
20. Hirsch,J.A. et al. (1999) The 2.8 Å crystal structure of visual arrestin: A model for arrestin's regulation. Cell, 97, 257-269.
21. Hubbard,T. et al. (2005) Ensembl 2005. Nucleic Acids Res., 33, D447-D453.
22. Kelly,P.A. and Rahmani,Z. (2005) DYRK1A enhances the mitogen-activated protein kinase cascade in PC12 cells by forming a complex with Ras, B-Raf, and MEK1. Mol. Biol. Cell, 16, 3562-3573.
23. Lefkowitz,R.J. and Whalen,E.J. (2004) beta-arrestins: Traffic cops of cell signalling. Curr. Opin. Cell Biol., 16, 162-168.
24. Lin,J.H. et al. (1999) The ankyrin repeat-containing adaptor protein Tvl-1 is a novel substrate and regulator of Raf-1. J. Biol. Chem., 274, 14706-14715.
25. Manning,G. et al. (2002) The protein kinase complement of the human genome. Science, 298, 1912-1934.
26. McGuffin,L.J. and Jones,D.T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19, 874-881.
27. Meylan,E. et al. (2002) RIP4 (DIK/PIKK), a novel member of the RIP kinase family, activates NF-kB and is processed during apoptosis. EMBO reports, 3, 1202-1208.
28. Meylan,E. and Tschopp,J. (2005) The RIP kinases: Crucial integrators of cellular stress. Trends Biochem. Sci., 30, 151-159.
29. Miyata,Y. and Nishida,E. (1999) Distantly related cousins of MAP kinase: biochemical properties and possible physiological functions. Biochem. Biophys. Res. Commun., 266, 291-295.
30. Mosavi,L.K. et al. (2004) The ankyrin repeat as molecular architecture for protein recognition. Protein Sci., 13, 1435-1448.
31. Nikolaienko,O. et al. (2005) Human chromosome 21/Down syndrome gene function and pathway database. Gene, 364, 90-98.
32. Pruitt,K.D. et al. (2005) NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.
33. Rychlewski,L. and Fischer,D. (2005) LiveBench-8: The large-scale, continuous assessment of automated protein structure prediction. Protein Sci., 14, 240-245.
34. Swatton,J.E. et al. (2004) Increased MAP kinase activity in Alzheimer's and Down syndrome but not in schizophrenia human brain. Eur. J. Neurosci., 19, 2711-2719.
35. Thompson,J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
36. Whitmarsh,A.J. and Davis,R.J. (1998) Structural organization of MAP-kinase signalling modules by scaffold proteins in yeast and mammals. Trends Biochem. Sci., 23, 481-485.