Article (Scientific journals)
IDARE2-Simultaneous Visualisation of Multiomics Data in Cytoscape.
Pfau, Thomas; Galhardo, Mafalda; Lin, Jake et al.
2021In Metabolites, 11 (5)
Peer Reviewed verified by ORBi
 

Files


Full Text
metabolites-11-00300-v2.pdf
Publisher postprint (972.13 kB)
Download

All documents in ORBilu are protected by a user license.

Send to



Details



Keywords :
data visualisation; metabolic networks; network structure
Abstract :
[en] Visual integration of experimental data in metabolic networks is an important step to understanding their meaning. As genome-scale metabolic networks reach several thousand reactions, the task becomes more difficult and less revealing. While databases like KEGG and BioCyc provide curated pathways that allow a navigation of the metabolic landscape of an organism, it is rather laborious to map data directly onto those pathways. There are programs available using these kind of databases as a source for visualization; however, these programs are then restricted to the pathways available in the database. Here, we present IDARE2 a cytoscape plugin that allows the visualization of multiomics data in cytoscape in a user-friendly way. It further provides tools to disentangle highly connected network structures based on common properties of nodes and retains structural links between the generated subnetworks, offering a straightforward way to traverse the splitted network. The tool is extensible, allowing the implementation of specialised representations and data format parsers. We present the automated reproduction of the original IDARE nodes using our tool and show examples of other data being mapped on a network of E. coli. The extensibility is demonstrated with two plugins that are available on github. IDARE2 provides an intuitive way to visualise data from multiple sources and allows one to disentangle the often complex network structure in large networks using predefined properties of the network nodes.
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Pfau, Thomas
Galhardo, Mafalda
Lin, Jake
Sauter, Thomas ;  University of Luxembourg > Faculty of Science, Technology and Medicine (FSTM) > Department of Life Sciences and Medicine (DLSM)
External co-authors :
yes
Language :
English
Title :
IDARE2-Simultaneous Visualisation of Multiomics Data in Cytoscape.
Publication date :
2021
Journal title :
Metabolites
ISSN :
2218-1989
Publisher :
MDPI AG, Basel, Switzerland
Volume :
11
Issue :
5
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 21 June 2021

Statistics


Number of views
78 (4 by Unilu)
Number of downloads
52 (1 by Unilu)

Scopus citations®
 
2
Scopus citations®
without self-citations
2
OpenCitations
 
2
WoS citations
 
2

Bibliography


Similar publications



Contact ORBilu