ArticleBioinformatics (Oxford, England)2011
Sorting the nuclear proteome.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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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.
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Who cites it
11 citing papers in PubMed, 22 citations in OpenAlex.
- Article
- Detailed prediction of protein sub-nuclear localization.BMC bioinformatics · 2019Article
- Nuclear Proteomics Uncovers Diurnal Regulatory Landscapes in Mouse Liver.Cell metabolism · 2017Article
- Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments.International journal of molecular sciences · 2015Article
- A Crowdsourced nucleus: understanding nuclear organization in terms of dynamically networked protein function.Biochimica et biophysica acta · 2014Review
- Genomic characterization of the mouse ribosomal DNA locus.G3 (Bethesda, Md.) · 2014Article
- NSort/DB: an intranuclear compartment protein database.Genomics, proteomics & bioinformatics · 2012Article
- Mapping the stabilome: a novel computational method for classifying metabolic protein stability.BMC systems biology · 2012Article
- Activation of intracellular metabotropic glutamate receptor 5 in striatal neurons leads to up-regulation of genes associated with sustained synaptic transmission including Arc/Arg3.1 protein.The Journal of biological chemistry · 2012Article
- ELM--the database of eukaryotic linear motifs.Nucleic acids research · 2012Article
- CellOrganizer: Image-derived models of subcellular organization and protein distribution.Methods in cell biology · 2012Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
Abstract
motivationQuantitative experimental analyses of the nuclear interior reveal a morphologically structured yet dynamic mix of membraneless compartments. Major nuclear events depend on the functional integrity and timely assembly of these intra-nuclear compartments. Yet, unknown drivers of protein mobility ensure that they are in the right place at the time when they are needed.
resultsThis study investigates determinants of associations between eight intra-nuclear compartments and their proteins in heterogeneous genome-wide data. We develop a model based on a range of candidate determinants, capable of mapping the intra-nuclear organization of proteins. The model integrates protein interactions, protein domains, post-translational modification sites and protein sequence data. The predictions of our model are accurate with a mean AUC (over all compartments) of 0.71. We present a complete map of the association of 3567 mouse nuclear proteins with intra-nuclear compartments. Each decision is explained in terms of essential interactions and domains, and qualified with a false discovery assessment. Using this resource, we uncover the collective role of transcription factors in each of the compartments. We create diagrams illustrating the outcomes of a Gene Ontology enrichment analysis. Associated with an extensive range of transcription factors, the analysis suggests that PML bodies coordinate regulatory immune responses.
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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.