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2016 ; 5
(ä): 1745
Nephropedia Template TP
gab.com Text
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English Wikipedia
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually
relevant hubs in biological networks
#MMPMID27853512
Muetze T
; Goenawan IH
; Wiencko HL
; Bernal-Llinares M
; Bryan K
; Lynn DJ
F1000Res
2016[]; 5
(ä): 1745
PMID27853512
show ga
Highly connected nodes (hubs) in biological networks are topologically important
to the structure of the network and have also been shown to be preferentially
associated with a range of phenotypes of interest. The relative importance of a
hub node, however, can change depending on the biological context. Here, we
report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables
users to easily construct and visualize a network of interactions from a gene or
protein list of interest, integrate contextual information, such as gene
expression or mass spectrometry data, and identify hub nodes that are more highly
connected to contextual nodes (e.g. genes or proteins that are differentially
expressed) than expected by chance. In a case study, we use CHAT to construct a
network of genes that are differentially expressed in Dengue fever, a viral
infection. CHAT was used to identify and compare contextual and degree-based hubs
in this network. The top 20 degree-based hubs were enriched in pathways related
to the cell cycle and cancer, which is likely due to the fact that proteins
involved in these processes tend to be highly connected in general. In
comparison, the top 20 contextual hubs were enriched in pathways commonly
observed in a viral infection including pathways related to the immune response
to viral infection. This analysis shows that such contextual hubs are
considerably more biologically relevant than degree-based hubs and that analyses
which rely on the identification of hubs solely based on their connectivity may
be biased towards nodes that are highly connected in general rather than in the
specific context of interest. AVAILABILITY: CHAT is available for Cytoscape 3.0+
and can be installed via the Cytoscape App Store (
http://apps.cytoscape.org/apps/chat).
free
free
free
