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MONGKIE: an integrated tool for network analysis and visualization for multi-omics data

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Authors
Jang, Yeongjun; Yu, Namhee; Seo, Jihae; Kim, Sun; Lee, Sanghyuk
Issue Date
2016-03-18
Publisher
BioMed Central
Citation
Biology Direct, 11(1):10
Keywords
Network visualizationNetwork modelingGraph clusteringOmics data analysisOver-representation analysis
Abstract
Background
Network-based integrative analysis is a powerful technique for extracting biological insights from multilayered omics data such as somatic mutations, copy number variations, and gene expression data. However, integrated analysis of multi-omics data is quite complicated and can hardly be done in an automated way. Thus, a powerful interactive visual mining tool supporting diverse analysis algorithms for identification of driver genes and regulatory modules is much needed.

Results
Here, we present a software platform that integrates network visualization with omics data analysis tools seamlessly. The visualization unit supports various options for displaying multi-omics data as well as unique network models for describing sophisticated biological networks such as complex biomolecular reactions. In addition, we implemented diverse in-house algorithms for network analysis including network clustering and over-representation analysis. Novel functions include facile definition and optimized visualization of subgroups, comparison of a series of data sets in an identical network by data-to-visual mapping and subsequent overlaying function, and management of custom interaction networks. Utility of MONGKIE for network-based visual data mining of multi-omics data was demonstrated by analysis of the TCGA glioblastoma data. MONGKIE was developed in Java based on the NetBeans plugin architecture, thus being OS-independent with intrinsic support of module extension by third-party developers.

Conclusion
We believe that MONGKIE would be a valuable addition to network analysis software by supporting many unique features and visualization options, especially for analysing multi-omics data sets in cancer and other diseases.

Reviewers
This article was reviewed by Prof. Limsoon Wong, Prof. Soojin Yi, and Maciej M Kańduła (nominated by Prof. David P Kreil).
Language
English
URI
https://hdl.handle.net/10371/109872
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College of Natural Sciences (자연과학대학)Program in Bioinformatics (협동과정-생물정보학전공)Journal Papers (저널논문_협동과정-생물정보학전공)
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