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

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 a...

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Bibliographic Details
Published in:Biology direct 2016-03, Vol.11 (1), p.10-10, Article 10
Main Authors: Jang, Yeongjun, Yu, Namhee, Seo, Jihae, Kim, Sun, Lee, Sanghyuk
Format: Article
Language:English
Subjects:
Algorithms
Analysis
Application Note
Computational Biology
Data mining
DNA Copy Number Variations - genetics
Gene expression
Gliomas
Software
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Summary: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. 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. 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. .
ISSN:1745-6150
1745-6150
DOI:10.1186/s13062-016-0112-y