A new parameter to study compositional properties of non-coding regions in eukaryotic genomes

Gene

Volumn 385, Issue , 2006, Pages 75-82

  Bultrini, Emanuele ^a   Pizzi, Elisabetta ^a  

^a ISTITUTO SUPERIORE DI SANITÀ   (Italy)

Author keywords

C. elegans; D. melanogaster; Eukaryotic promoters; H. sapiens; Linear discriminant analysis; M. musculus; Principal component analysis

Indexed keywords

OLIGONUCLEOTIDE;

ARTICLE; EUKARYOTIC CELL; GENE SEQUENCE; GENOME; HUMAN; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; TRANSCRIPTION INITIATION;

ANIMALS; BASE COMPOSITION; CAENORHABDITIS ELEGANS; DISCRIMINANT ANALYSIS; DROSOPHILA MELANOGASTER; EXONS; HUMANS; INTRONS; LINEAR MODELS; MICE; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; PRINCIPAL COMPONENT ANALYSIS; PROMOTER REGIONS (GENETICS); RNA, UNTRANSLATED; SPECIES SPECIFICITY;

CAENORHABDITIS ELEGANS; DROSOPHILA MELANOGASTER; EUKARYOTA; HOMO SAPIENS; MUS MUSCULUS;

EID: 37849187203     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.05.030     Document Type: Article

References (31)

1. Aerts S., Thijs G., Dabrowski M., Moreau Y., and De Moor B. Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics 5 (2004) 34
2. Alexander G., Tatyana P., and Zinovyev A. Four basic symmetry types in the universal 7-cluster structure of 143 complete bacterial genomic sequences. In Silico Biol. 5 (2005) 0025
3. Baronchelli A., Caglioti E., Loreto V., and Pizzi E. Dictionary based methods for information extraction. Physica, A 342 (2004) 294-300
4. Bernardi G. The human genome: organization and evolutionary history. Annu. Rev. Genet. 29 (1995) 445-476
5. Bernardi G. Isochores and the evolutionary genomics of vertebrates. Gene 241 (2000) 3-17
6. Bernardi G. The compositional evolution of vertebrate genomes. Gene 259 (2000) 31-43
7. Bultrini E., Pizzi E., Del Giudice P., and Frontali C. Pentamer vocabularies characterizing introns and intron-like intergenic tracts from Caenorhabditis elegans and Drosophila melanogaster. Gene 304 (2003) 183-192
8. Brazma A., Jonassen I., and Ukkonen E. Predicting gene regulatory elements in silico on a genomic scale. Genome Res. 8 (1998) 1202-1215
9. Campbell A., Mrazek J., and Karlin S. Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc. Natl. Acad. Sci. U. S. A. 96 (1999) 9184-9189
10. Carbone A., Kepes F., and Zinovyev A. Codon bias signatures, organization of microorganisms in codon space, and lifestyle. Mol. Biol. Evol. 22 (2005) 547-561
11. Chapus C., Dufraigne C., Edwards S., Giron A., Fertil B., and Deschavanne P. Exploration of phylogenetic data using a global sequence analysis method. BMC Evol. Biol. 5 (2005) 63
12. Cora D., Di Cunto F., Provero P., Silengo L., and Caselle M. Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing over-represented upstream motifs. BMC Bioinformatics 11 (2004) 5
13. Cruveiller S., Jabbari K., Clay O., and Bernardi G. Compositional features of eukaryotic genomes for checking predicted genes. Brief Bioinform. 4 (2003) 43-52
14. Foerstner K.U., von Mering C., Hooper S.D., and Bork P. Environments shape the nucleotide composition of genomes. EMBO Rep. 6 (2005) 1208-1213
15. Frontali C., and Pizzi E. Similarity in oligonucleotide usage in introns and intergenic regions contributes to long-range correlation in the Caenorhabditis elegans genome. Gene 232 (1999) 87-95
16. Gentles A.J., and Karlin S. Genome-scale compositional comparisons in eukaryotes. Genome Res. 11 (2001) 540-546
17. Grantham R., Gautier C., Gouy M., Mercier R., and Pave A. Codon catalog usage and the genome hypothesis. Nucleic Acids Res. 8 (1980) 49-62
18. Hannenalli S., and Levy S. Promoter prediction in the human genome. Bioinformatics 17 (2001) 90-96
19. Kanhere A., and Bansal M. Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes. Nucleic Acids Res. 33 (2005) 3165-3175
20. Karlin S., and Ladunga I. Comparisons of eukaryotic genomic sequences. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 12832-12836
21. Kel-Margoulis O.V., et al. Composition-sensitive analysis of the human genome for regulatory signals. In Silico Biol. 3 (2003) 145-171
22. Mariño-Ramirez L., Spouge J.L., Kanga G.C., and Landsman D. Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res. 32 (2004) 949-958
23. Munteanu M.G., Vlahovicek K., Parthasaraty S., Simon I., and Pongor S. Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena. Trends Biochem. Sci. 23 (1998) 341-346
24. Nekrutenko A., and Li W.H. Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res. 10 (2000) 1986-1995
25. Ohler U., Niemann H., Liao G., and Rubin G.M. Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics 17 (2001) S199-S206
26. Pedersen A.G., Baldi P., Chauvin Y., and Brunak S. The biology of eukaryotic promoter prediction - a review. Comput. Chem. 15 (1999) 191-207
27. Périer R.C., Praz V., Junier T., Bonnard C., and Bucher P. The Eukaryotic Promoter Database (EPD). Nucleic Acids Res. 28 (2000) 302-303
28. Saxonov S., Daizadeh I., Fedorov A., and Gilbert W. EID: the Exon-Intron Database-an exhaustive database of protein-coding intron-containing genes. Nucleic Acids Res. 28 (2000) 185-190
29. Suzuki Y., Yamashita R., Sugano S., and Nakai K. DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res. 32 (2004) D78-D81
30. Van Helden J., Andre B., and Collado-Vides J. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol. 281 (1998) 827-842
31. Wolfsberg T.G., Gabrielian A.E., Campbell M.J., Cho R.J., Spouge J.L., and Landsman D. Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae. Genome Res. 9 (1999) 775-792