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

Title
MONGKIE: An integrated tool for network analysis and visualization for multi-omics data
Authors
Jang Y.Yu N.Seo J.Kim S.Lee S.
Ewha Authors
이상혁
SCOPUS Author ID
이상혁scopus
Issue Date
2016
Journal Title
Biology Direct
ISSN
1745-6150JCR Link
Citation
Biology Direct vol. 11, no. 1
Keywords
Graph clusteringNetwork modelingNetwork visualizationOmics data analysisOver-representation analysis
Publisher
BioMed Central Ltd.
Indexed
SCIE; SCOPUS WOS scopus
Document Type
Article
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). © 2016 Jang et al.
DOI
10.1186/s13062-016-0112-y
Appears in Collections:
자연과학대학 > 생명과학전공 > Journal papers
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