ArticleGenome research2002
Shannon information theoretic computation of synonymous codon usage biases in coding regions of human and mouse genomes.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
24 citing papers in PubMed, 60 citations in OpenAlex.
- How Does Genetic Information Enable Life?Bulletin of mathematical biology · 2026Article
- Statistical analysis of synonymous and stop codons in pseudo-random and real sequences as a function of GC content.Scientific reports · 2023Article
- A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses.Gene reports · 2021Article
- Information theoretic perspective on genome clustering.Saudi journal of biological sciences · 2021Article
- Article
- A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data.International journal of molecular sciences · 2015Article
- Sex moderates the effects of the Sorl1 gene rs2070045 polymorphism on cognitive impairment and disruption of the cingulum integrity in healthy elderly.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2015Article
- Article
- Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly.PloS one · 2015Article
- System analysis of synonymous codon usage biases in archaeal virus genomes.Journal of theoretical biology · 2014Article
- The influence of flanking secondary structures on amino Acid content and typical lengths of 3/10 helices.International journal of proteomics · 2014Article
- Applying Shannon's information theory to bacterial and phage genomes and metagenomes.Scientific reports · 2013Article
- Translational selection of genes coding for perfectly conserved proteins among three mosquito vectors.Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2012Article
- Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.BMC bioinformatics · 2012Article
- Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.PloS one · 2012Article
- Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations.Journal of translational medicine · 2011Article
- Extreme dependence of gH and gL expression on ORF57 and association with highly unusual codon usage in rhesus monkey rhadinovirus.Journal of virology · 2008Article
- Article
- CodonO: codon usage bias analysis within and across genomes.Nucleic acids research · 2007Article
- Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria.EURASIP journal on bioinformatics & systems biology · 2007Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Exonic GC of human mRNA reference sequences (RefSeqs), as well as A, C, G, and T in codon position 3 are linearly correlated with genomic GC. These observations utilize information from the completed human genome sequence and a large, high-quality set of human and mouse coding sequences, and are in accord with similar determinations published by others. A Shannon Information Theoretic measure of bias in synonymous codon usage was developed. When applied to either human or mouse RefSeqs, this measure is nonlinearly correlated with genomic, exonic, and third codon position A, C, G, and T. Information values between orthologous mouse and human RefSeqs are linearly correlated: mouse = 0.092 + 0.55 human. Mouse genes were consistently placed in genomic regions whose GC content was closer to 50% than was the GC content of the human ortholog. Since the (nonlinear) information versus percent GC curve has a minimum at 50% GC and monotonically increases with increasing distance from 50% GC, this phenomenon directly results in the low slope of 0.55. This appears to be a manifestation of an evolutionary strategy for placement of genes in regions of the genome with a GC content that relates synonymous codon bias and protein folding.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.