Sorting the nuclear proteome

Bauer, Denis C., Willadsen, Kai, Buske, Fabian A., Lê Cao, Kim-Anh, Bailey, Timothy L., Dellaire, Graham and Bodén, Mikael (2011) Sorting the nuclear proteome. Bioinformatics, 27 13: i7-i14. doi:10.1093/bioinformatics/btr217

Author Bauer, Denis C.
Willadsen, Kai
Buske, Fabian A.
Lê Cao, Kim-Anh
Bailey, Timothy L.
Dellaire, Graham
Bodén, Mikael
Title Sorting the nuclear proteome
Journal name Bioinformatics   Check publisher's open access policy
ISSN 1367-4803
Publication date 2011-07-01
Sub-type Article (original research)
DOI 10.1093/bioinformatics/btr217
Volume 27
Issue 13
Start page i7
End page i14
Total pages 8
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2012
Language eng
Formatted abstract
Quantitative 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.

This 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.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article number: i7-i14

Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 9 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 12 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Mon, 03 Oct 2011, 14:23:10 EST by Kai Willadsen on behalf of School of Chemistry & Molecular Biosciences