Large scale comparative visualisation of regulatory networks with TRNDiff

Chua, Xin-Yi, Buckingham, Lawrence, Hogan, James M. and Novichkov, Pavel (2015). Large scale comparative visualisation of regulatory networks with TRNDiff. In: International Conference On Computational Science, ICCS 2015 - Computational Science at the Gates of Nature. International Conference on Computational Science, ICCS 2002, Amsterdam, The Netherlands, (713-724). 21-24 April, 2002. doi:10.1016/j.procs.2015.05.189


Author Chua, Xin-Yi
Buckingham, Lawrence
Hogan, James M.
Novichkov, Pavel
Title of paper Large scale comparative visualisation of regulatory networks with TRNDiff
Conference name International Conference on Computational Science, ICCS 2002
Conference location Amsterdam, The Netherlands
Conference dates 21-24 April, 2002
Proceedings title International Conference On Computational Science, ICCS 2015 - Computational Science at the Gates of Nature   Check publisher's open access policy
Journal name Procedia Computer Science   Check publisher's open access policy
Place of Publication Amsterdam, The Netherlands
Publisher Elsevier
Publication Year 2015
Sub-type Fully published paper
DOI 10.1016/j.procs.2015.05.189
Open Access Status DOI
ISSN 1877-0509
Volume 51
Issue 1
Start page 713
End page 724
Total pages 12
Language eng
Abstract/Summary The advent of Next Generation Sequencing (NGS) technologies has seen explosive growth in genomic datasets, and dense coverage of related organisms, supporting study of subtle, strain-specific variations as a determinant of function. Such data collections present fresh and complex challenges for bioinformatics, those of comparing models of complex relationships across hundreds and even thousands of sequences. Transcriptional Regulatory Network (TRN) structures document the influence of regulatory proteins called Transcription Factors (TFs) on associated Target Genes (TGs). TRNs are routinely inferred from model systems or iterative search, and analysis at these scales requires simultaneous displays of multiple networks well beyond those of existing network visualisation tools [1]. In this paper we describe TRNDiff, an open source system supporting the comparative analysis and visualization of TRNs (and similarly structured data) from many genomes, allowing rapid identification of functional variations within species. The approach is demonstrated through a small scale multiple TRN analysis of the Fur iron-uptake system of Yersinia, suggesting a number of candidate virulence factors; and through a larger study exploiting integration with the RegPrecise database (http://regprecise.lbl.gov; [2]) - a collection of hundreds of manually curated and predicted transcription factor regulons drawn from across the entire spectrum of prokaryotic organisms.
Keyword Bioinformatics
Regulatory networks
Transcription
Visualisation
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Conference Paper
Collection: Institute for Molecular Bioscience - Publications
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 0 times in Thomson Reuters Web of Science Article
Scopus Citation Count Cited 1 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Mon, 01 Aug 2016, 20:50:47 EST by Mary-Anne Marrington on behalf of Institute for Molecular Bioscience