CompNet: a GUI based tool for comparison of multiple biological interaction networks.
BACKGROUND
Network visualization and analysis tools aid in better understanding of complex biological systems. Furthermore, to understand the differences in behaviour of system(s) under various environmental conditions (e.g. stress, infection), comparing multiple networks becomes necessary. Such comparisons between multiple networks may help in asserting causation and in identifying key components of the studied biological system(s). Although many available network comparison methods exist, which employ techniques like network alignment and querying to compute pair-wise similarity between selected networks, most of them have limited features with respect to interactive visual comparison of multiple networks.


RESULTS
In this paper, we present CompNet - a graphical user interface based network comparison tool, which allows visual comparison of multiple networks based on various network metrics. CompNet allows interactive visualization of the union, intersection and/or complement regions of a selected set of networks. Different visualization features (e.g. pie-nodes, edge-pie matrix, etc.) aid in easy identification of the key nodes/interactions and their significance across the compared networks. The tool also allows one to perform network comparisons on the basis of neighbourhood architecture of constituent nodes and community compositions, a feature particularly useful while analyzing biological networks. To demonstrate the utility of CompNet, we have compared a (time-series) human gene-expression dataset, post-infection by two strains of Mycobacterium tuberculosis, overlaid on the human protein-protein interaction network. Using various functionalities of CompNet not only allowed us to comprehend changes in interaction patterns over the course of infection, but also helped in inferring the probable fates of the host cells upon infection by the two strains.


CONCLUSIONS
CompNet is expected to be a valuable visual data mining tool and is freely available for academic use from http://metagenomics.atc.tcs.com/compnet/ or http://121.241.184.233/compnet/.
Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411 013, Maharashtra, India.
Bhusan K
BK
Kuntal
Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411 013, Maharashtra, India.
Anirban
A
Dutta
Bio-Sciences R&D Division, TCS Research, Tata Consultancy Services Ltd., 54-B, Hadapsar Industrial Estate, Pune, 411 013, Maharashtra, India. sharmila.mande@tcs.com.
Sharmila S
SS
Mande
D020869:Gene Expression Profiling; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000502:physiology; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D012984:Software