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Genome Res
2004 May 01;145:886-92. doi: 10.1101/gr.2246704.
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Compositional gene landscapes in vertebrates.
Cruveiller S
,
Jabbari K
,
Clay O
,
Bernardi G
.
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The existence of a well conserved linear relationship between GC levels of genes' second and third codon positions (GC2, GC3) prompted us to focus on the landscape, or joint distribution, spanned by these two variables. In human, well curated coding sequences now cover at least 15%-30% of the estimated total gene set. Our analysis of the landscape defined by this gene set revealed not only the well documented linear crest, but also the presence of several peaks and valleys along that crest, a property that was also indicated in two other warm-blooded vertebrates represented by large gene databases, that is, mouse and chicken. GC2 is the sum of eight amino acid frequencies, whereas GC3 is linearly related to the GC level of the chromosomal region containing the gene. The landscapes therefore portray relations between proteins and the DNA environments of the genes that encode them.
Bernardi,
The mosaic genome of warm-blooded vertebrates.
1985, Pubmed,
Xenbase
Bernardi,
The mosaic genome of warm-blooded vertebrates.
1985,
Pubmed
,
Xenbase
Bernardi,
The human genome and its evolutionary context.
1986,
Pubmed
Bernardi,
The compositional evolution of vertebrate genomes.
2000,
Pubmed
Bernardi,
Misunderstandings about isochores. Part 1.
2001,
Pubmed
Carels,
Two classes of genes in plants.
2000,
Pubmed
Clay,
Human coding and noncoding DNA: compositional correlations.
1996,
Pubmed
Cortadas,
An analysis of the bovine genome by density gradient centrifugation: fractionation in Cs2SO4/3,6-bis(acetatomercurimethyl)dioxane density gradient.
1977,
Pubmed
Cruveiller,
Incorrectly predicted genes in rice?
2004,
Pubmed
Cruveiller,
Compositional features of eukaryotic genomes for checking predicted genes.
2003,
Pubmed
Cuny,
The major components of the mouse and human genomes. 1. Preparation, basic properties and compositional heterogeneity.
1981,
Pubmed
D'Onofrio,
Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins.
1991,
Pubmed
D'Onofrio,
A universal compositional correlation among codon positions.
1992,
Pubmed
D'Onofrio,
The correlation of protein hydropathy with the base composition of coding sequences.
1999,
Pubmed
Duret,
HOVERGEN: a database of homologous vertebrate genes.
1994,
Pubmed
Fields,
How many genes in the human genome?
1994,
Pubmed
Glusman,
The complete human olfactory subgenome.
2001,
Pubmed
Gouy,
ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage.
1985,
Pubmed
Grillo,
CLEANUP: a fast computer program for removing redundancies from nucleotide sequence databases.
1996,
Pubmed
Jabbari,
The correlation between GC3 and hydropathy in human genes.
2003,
Pubmed
Jabbari,
The new genes of rice: a closer look.
2004,
Pubmed
Jabbari,
The major shifts of human duplicated genes.
2003,
Pubmed
Macaya,
An approach to the organization of eukaryotic genomes at a macromolecular level.
1976,
Pubmed
Macaya,
An analysis of the bovine genome by density-gradient centrifugation. Preparation of the dG+dC-rich DNA components.
1978,
Pubmed
Musto,
Compositional correlations in the chicken genome.
1999,
Pubmed
Olofsson,
Organization of nucleotide sequences in the chicken genome.
1983,
Pubmed
Pavlícek,
A compact view of isochores in the draft human genome sequence.
2002,
Pubmed
Pruitt,
RefSeq and LocusLink: NCBI gene-centered resources.
2001,
Pubmed
SCHILDKRAUT,
Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl.
1962,
Pubmed
Saccone,
Localization of the gene-richest and the gene-poorest isochores in the interphase nuclei of mammals and birds.
2002,
Pubmed
Salamov,
Ab initio gene finding in Drosophila genomic DNA.
2000,
Pubmed
Sueoka,
Directional mutation pressure and neutral molecular evolution.
1988,
Pubmed
Venter,
The sequence of the human genome.
2001,
Pubmed
Zoubak,
The gene distribution of the human genome.
1996,
Pubmed