ArticleMolecular systems biology2019
Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues.
Article in Molecular systems biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 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
54 citing papers in PubMed.
- Proteome-Transcriptome Discordance in Rice Under Drought Is Modulated by Post-Translational Modifications with Functional Consequences for Photosynthesis and Energy Metabolism.Plants (Basel, Switzerland) · 2026Article
- Strategies for constructing context-specific protein-protein interaction networks.Briefings in bioinformatics · 2026Review
- Predicting the translation efficiency of messenger RNA in mammalian cells.Nature biotechnology · 2026Article
- Paired-Box (PAX) Gene Signatures as a Biomarker of Breast Cancer Progression.International journal of molecular sciences · 2026Article
- Integrated analysis of post-transcriptional regulations reveals insights into acute myeloid leukemia.Communications biology · 2025Article
- Principles of protein abundance regulation across single cells in a mammalian tissue.bioRxiv : the preprint server for biology · 2025Article
- Dynamics of Single-Cell Protein Covariation during Epithelial-Mesenchymal Transition.Journal of proteome research · 2025Article
- Inferring protein from transcript abundances using convolutional neural networks.BioData mining · 2025Article
- mRNA vaccine sequence and structure design and optimization: Advances and challenges.The Journal of biological chemistry · 2025Review
- TExCNN: Leveraging Pre-Trained Models to Predict Gene Expression from Genomic Sequences.Genes · 2024Article
- Proteome-wide copy-number estimation from transcriptomics.Molecular systems biology · 2024Article
- Inferring post-transcriptional regulation within and across cell types in human testis.bioRxiv : the preprint server for biology · 2024Article
- Integrative Analysis of Multi-Omics Data to Identify Deregulated Molecular Pathways and Druggable Targets in Chronic Lymphocytic Leukemia.Journal of personalized medicine · 2024Article
- Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of NNature plants · 2024Article
- Multi-Omic Analysis of Esophageal Adenocarcinoma Uncovers Candidate Therapeutic Targets and Cancer-Selective Posttranscriptional Regulation.Molecular & cellular proteomics : MCP · 2024Article
- Instrumentation at the Leading Edge of Proteomics.Analytical chemistry · 2024Review
- Dynamics of single-cell protein covariation during epithelial-mesenchymal transition.bioRxiv : the preprint server for biology · 2024Article
- Review
- Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein-to-mRNA (PTR) ratios and a quantification of their effects are still lacking. Here, we quantified PTR ratios for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We estimated by regression the contribution of known sequence determinants of protein synthesis and degradation in addition to 45 mRNA and 3 protein sequence motifs that we found by association testing. While PTR ratios span more than 2 orders of magnitude, our integrative model predicts PTR ratios at a median precision of 3.2-fold. A reporter assay provided functional support for two novel UTR motifs, and an immobilized mRNA affinity competition-binding assay identified motif-specific bound proteins for one motif. Moreover, our integrative model led to a new metric of codon optimality that captures the effects of codon frequency on protein synthesis and degradation. Altogether, this study shows that a large fraction of PTR ratio variation in human tissues can be predicted from sequence, and it identifies many new candidate post-transcriptional regulatory elements.
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.