ArticleProceedings of the National Academy of Sciences of the United States of America2010
Identification of differential translation in genome wide studies.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 80 citations in OpenAlex.
- Allele-specific expression is associated with lower translational efficiency in mouse embryos and stem cells.bioRxiv : the preprint server for biology · 2026Article
- Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue.Nature communications · 2026Article
- Translation efficiency covariation identifies conserved coordination patterns across cell types.Nature biotechnology · 2026Article
- Predicting the translation efficiency of messenger RNA in mammalian cells.Nature biotechnology · 2026Article
- Translational buffering tunes gene expression in mice and humans.Genome biology · 2026Article
- Capturing Translation in Action with Protein Synthesis Profiling.bioRxiv : the preprint server for biology · 2025Article
- CXXC5 is a ubiquitinated protein and is degraded by the ubiquitin-proteasome pathway.Protein science : a publication of the Protein Society · 2025Article
- Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast.Nucleic acids research · 2024Article
- Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2).NAR cancer · 2022Article
- Deadenylase-dependent mRNA decay of GDF15 and FGF21 orchestrates food intake and energy expenditure.Cell metabolism · 2022Article
- Article
- An integrative approach to assessing effects of a short-term Western diet on gene expression in rat liver.Frontiers in endocrinology · 2022Article
- Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein.RNA (New York, N.Y.) · 2021Article
- Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density.Nature methods · 2021Article
- Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein.bioRxiv : the preprint server for biology · 2021Article
- A PRC2-independent function for EZH2 in regulating rRNA 2'-O methylation and IRES-dependent translation.Nature cell biology · 2021Article
- Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis.The Plant cell · 2020Article
- Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression.The EMBO journal · 2019Article
- Translational regulation contributes to the secretory response of chondrocytic cells following exposure to interleukin-1β.The Journal of biological chemistry · 2019Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Regulation of gene expression through translational control is a fundamental mechanism implicated in many biological processes ranging from memory formation to innate immunity and whose dysregulation contributes to human diseases. Genome wide analyses of translational control strive to identify differential translation independent of cytosolic mRNA levels. For this reason, most studies measure genes' translation levels as log ratios (translation levels divided by corresponding cytosolic mRNA levels obtained in parallel). Counterintuitively, arising from a mathematical necessity, these log ratios tend to be highly correlated with the cytosolic mRNA levels. Accordingly, they do not effectively correct for cytosolic mRNA level and generate substantial numbers of biological false positives and false negatives. We show that analysis of partial variance, which produces estimates of translational activity that are independent of cytosolic mRNA levels, is a superior alternative. When combined with a variance shrinkage method for estimating error variance, analysis of partial variance has the additional benefit of having greater statistical power and identifying fewer genes as translationally regulated resulting merely from unrealistically low variance estimates rather than from large changes in translational activity. In contrast to log ratios, this formal analytical approach estimates translation effects in a statistically rigorous manner, eliminates the need for inefficient and error-prone heuristics, and produces results that agree with biological function. The method is applicable to datasets obtained from both the commonly used polysome microarray method and the sequencing-based ribosome profiling method.
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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.