ArticleGenome biology2013
Transcriptome and proteome quantification of a tumor model provides novel insights into post-transcriptional gene regulation.
Article in Genome biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 58 citations in OpenAlex.
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- The TRIM-NHL RNA-binding protein Brain Tumor coordinately regulates expression of the glycolytic pathway and vacuolar ATPase complex.Nucleic acids research · 2024Article
- Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model.Cell genomics · 2024Article
- Comparative modeling reveals the molecular determinants of aneuploidy fitness cost in a wild yeast model.bioRxiv : the preprint server for biology · 2024Article
- Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast.Nucleic acids research · 2024Article
- Proteotype coevolution and quantitative diversity across 11 mammalian species.Science advances · 2022Article
- Autosomal dominant optic atrophy: A novel treatment forMolecular therapy. Nucleic acids · 2021Article
- Molecular and biological functions of TRIM-NHL RNA-binding proteins.Wiley interdisciplinary reviews. RNA · 2021Review
- Identification of critical pathways and potential therapeutic targets in poorly differentiated duodenal papilla adenocarcinoma.Cancer cell international · 2021Article
- Convergent network effects along the axis of gene expression during prostate cancer progression.Genome biology · 2020Article
- StanDep: Capturing transcriptomic variability improves context-specific metabolic models.PLoS computational biology · 2020Article
- An Integrated Transcriptomic and Proteomic Analysis Identifies Significant Novel Pathways for Henoch-Schönlein Purpura Nephritis Progression.BioMed research international · 2020Article
- Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses.Hereditas · 2019Article
- The asymmetrically segregating lncRNA cherub is required for transforming stem cells into malignant cells.eLife · 2018Article
- A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor ineLife · 2018Article
- Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells.Nature communications · 2017Article
- Phosphoenolpyruvate Carboxykinase Maintains Glycolysis-driven Growth in Drosophila Tumors.Scientific reports · 2017Article
- Proteome and Secretome Analysis Reveals Differential Post-transcriptional Regulation of Toll-like Receptor Responses.Molecular & cellular proteomics : MCP · 2017Article
Corrections and comments
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Authors and funding
8 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome-wide transcriptome analyses have given systems-level insights into gene regulatory networks. Due to the limited depth of quantitative proteomics, however, our understanding of post-transcriptional gene regulation and its effects on protein-complex stoichiometry are lagging behind.
resultsHere, we employ deep sequencing and the isobaric tag for relative and absolute quantification (iTRAQ) technology to determine transcript and protein expression changes of a Drosophila brain tumor model at near genome-wide resolution. In total, we quantify more than 6,200 tissue-specific proteins, corresponding to about 70% of all transcribed protein-coding genes. Using our integrated data set, we demonstrate that post-transcriptional gene regulation varies considerably with biological function and is surprisingly high for genes regulating transcription. We combine our quantitative data with protein-protein interaction data and show that post-transcriptional mechanisms significantly enhance co-regulation of protein-complex subunits beyond transcriptional co-regulation. Interestingly, our results suggest that only about 11% of the annotated Drosophila protein complexes are co-regulated in the brain. Finally, we refine the composition of some of these core protein complexes by analyzing the co-regulation of potential subunits.
conclusionsOur comprehensive transcriptome and proteome data provide a valuable resource for quantitative biology and offer novel insights into understanding post-transcriptional gene regulation in a tumor model.
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