ArticleDatabase : the journal of biological databases and curation2012
The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes.
Article in Database : the journal of biological databases and curation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed.
- G/C-ending and synonymous codon bias define functional translational programs that shape human tissue and cancer proteomes.NAR genomics and bioinformatics · 2026Article
- Genes and Pathways Comprising the Human and Mouse ORFeomes Display Distinct Codon Bias Signatures that Can Regulate Protein Levels.bioRxiv : the preprint server for biology · 2025Article
- Decoding Codon Bias: The Role of tRNA Modifications in Tissue-Specific Translation.International journal of molecular sciences · 2025Article
- Dynamic mRNA Stability Buffer Transcriptional Activation During Neuronal Differentiation and Is Regulated by SAMD4A.Journal of cellular physiology · 2025Article
- SARS-CoV-2 Displays a Suboptimal Codon Usage Bias for Efficient Translation in Human Cells Diverted by Hijacking the tRNA Epitranscriptome.International journal of molecular sciences · 2024Article
- Translational response to mitochondrial stresses is orchestrated by tRNA modifications.bioRxiv : the preprint server for biology · 2024Article
- Dysfunctional tRNA reprogramming and codon-biased translation in cancer.Trends in molecular medicine · 2022Review
- Codon Usage and mRNA Stability are Translational Determinants of Cellular Response to Canonical Ferroptosis Inducers.Neuroscience · 2022Article
- Abundances of transcripts, proteins, and metabolites in the cell cycle of budding yeast reveal coordinate control of lipid metabolism.Molecular biology of the cell · 2020Article
- Article
- tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence.Nature communications · 2016Article
- Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool.Methods (San Diego, Calif.) · 2016Article
- Global translational impacts of the loss of the tRNA modification tMicrobial cell (Graz, Austria) · 2016Article
- Essentiality of threonylcarbamoyladenosine (t(6)A), a universal tRNA modification, in bacteria.Molecular microbiology · 2015Article
- Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes.Chemical research in toxicology · 2015Article
- Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats.RNA (New York, N.Y.) · 2015Article
- Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses.RNA biology · 2015Review
- A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications.Methods in enzymology · 2015Article
- tRNA modifications regulate translation during cellular stress.FEBS letters · 2014Review
- A system of RNA modifications and biased codon use controls cellular stress response at the level of translation.Chemical research in toxicology · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
A codon consists of three nucleotides and functions during translation to dictate the insertion of a specific amino acid in a growing peptide or, in the case of stop codons, to specify the completion of protein synthesis. There are 64 possible single codons and there are 4096 double, 262 144 triple, 16 777 216 quadruple and 1 073 741 824 quintuple codon combinations available for use by specific genes and genomes. In order to evaluate the use of specific single, double, triple, quadruple and quintuple codon combinations in genes and gene networks, we have developed a codon counting tool and employed it to analyze 5780 Saccharomyces cerevisiae genes. We have also developed visualization approaches, including codon painting, combination and bar graphs, and have used them to identify distinct codon usage patterns in specific genes and groups of genes. Using our developed Gene-Specific Codon Counting Database, we have identified extreme codon runs in specific genes. We have also demonstrated that specific codon combinations or usage patterns are over-represented in genes whose corresponding proteins belong to ribosome or translation-associated biological processes. Our resulting database provides a mineable list of multi-codon data and can be used to identify unique sequence runs and codon usage patterns in individual and functionally linked groups of genes.
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.