Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

HiVis: a portable, scalable tool for hierarchical visualization and analysis of biological networks

HiVis: a portable, scalable tool for hierarchical visualization and analysis of biological networks tushikui@sjtu.edu.cn Department of Computer It is very important to analyze the network structure of interacting genes, proteins, Science and Engineering, RNAs, etc. in large-scale biological networks which represent complex biological School of Electronic Information and Electrical systems. Many tools have been made for this purpose. However, they are either unable Engineering, Shanghai to display the hierarchically structured view of the networks or not easy to build in Jiao Tong University, cross-platforms. Here, we present a navigation tool called HiVis for biological network 800 Dongchuan Road, Shanghai 200240, China visualization. HiVis provides a hierarchical view of the networks through a zoom-in or Full list of author information zoom-out function powered by k-means and fast approximate spectral clustering algo- is available at the end of the rithms. It is a cross-platform, portable, fast desktop application to large-scale networks. article Keywords: Hierarchical visualization, Cross-platform, Clustering algorithms Background To the Editor: motivated by HiMap (Shi et al. 2009), we present HiVis, an open-source software that provides hierarchical interactive visualization and analysis for biological networks. It contains three main features: • Not only is it able to visualize networks which contain tens of thousands interactions in a hierarchically structured way, but also it allows the analysis of the local connec- tions centered on a specific element. • It provides a suite of interactive methods for the user to analyze structural detail of the network. • HiVis is a portable cross-platform application, so that users do not need to go through the tedious installation process and bothered by installing a lot of dependent packages. Methods We use a top-down approach to cluster the biological networks into a multi-level node- link graph. We demonstrate the main features in Fig. 1 through a data set from STRING interaction database (https ://strin g-db.org/cgi/input .pl). It is well known that many bio- logical networks contain clique and hub genes which are highly clustered and contain © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat iveco mmons .org/licen ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Qiang et al. Appl Inform (2018) 5:3 Page 2 of 3 Fig. 1 Illustration of features in HiVis, a software that provides hierarchical visualization and analysis of biological networks. a The interface of HiVis; b The full scope of the nodes inside the selected cluster in (a); c Displaying the selcted gene, its most related ones and their interactions when choosing a gene in (a); d Displaying the network by a fast approximate spectral clustering method in each hierarchy self-similar structure. Therefore, clustering them together into one node can reveal their hierarchical information and make the visualization readable. Currently, we provide two cluster algorithms, k-means clustering, and fast approxi- mate spectral clustering (Yan et al. 2009), which is faster than normal spectral clustering method and is more suitable for network clustering than k-means algorithm. The idea is to use k-means as a preprocessor and then to perform the normal spectral clustering method. Here, we also implemented a heuristic approach to determine the number of clusters by checking the slope of neighboring points of sorted eigenvalues. Implementation It is difficult to display the biological network meaningfully in one scope, HiVis solves it by cluster them into a hierarchical tree and only reveal the nodes in the current view and the view in the next hierarchy. To be more specific, here, we present an example illus - trated in Fig. 1, 1a is the overview of HiVis, the genes are clustered using k-means, and each node represents a group of them. It can switch the algorithm to modified spectral clustering and the result is shown in Fig.  1d. HiVis offers smooth animation methods to further analyze the computed clusters. When selecting one cluster, it will show a full scope of its inner structure; as shown in Fig.  1b, users can also return to the previous stage, or they can further analyze the current cluster with the same procedure. Apart from that HiVis will show each genes within the cluster, as is shown in the left part of Qiang et al. Appl Inform (2018) 5:3 Page 3 of 3 Fig. 1b, when choosing one gene, HiVis will display the gene and its most related genes in a network, as is shown in Fig. 1c. Thus, it will help to analyze the network locally. Conclusion In this paper, we present HiVis, a software built on electron for hierarchical visualiza- tion and analysis of biological networks. We implemented the k-means clustering, fast approximate spectral clustering algorithm, and force-direct layout algorithm to let HiVis capable of handling large-scale biological data. It is worth noting that this kind of dis- playing technique is very general and can be applied to other networks like social net- work, security network, etc. Authors’ contributions The authors discussed the problem and the solutions were proposed all together. All authors participated in drafting and revising the final manuscript. All authors read and approved the final manuscript. Author details Department of Computer Science and Engineering, School of Electronic Information and Electrical Engineering, Shang- hai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China. Bioinformatics Program, Boston University, Boston 02215, USA. School of Computer Science, Carnegie Mellon University, Pittsburgh 15213, USA. Acknowledgements The work is supported by a starting grant ( WF220403029) from Shanghai Jiao Tong University. Competing interests The authors declare that they have no competing interests. Availability of data and materials The installation package and source code can be accessed at https ://githu b.com/QLigh tman/HiVis . Ethics approval and consent to participate Not applicable. Funding Not applicable. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Received: 7 May 2018 Accepted: 31 May 2018 References Protein–protein interaction networks. https ://strin g-db.org/cgi/input .pl Shi L, Cao N, Liu SX, Qian WH, Tan L, Wang GD, Sun JM, Lin CY (2009) HiMap: adaptive visualization of large-scale online social networks. In: Proceedings of IEEE Pacific visualization symposium 2009 (PacificVis’09), Beijing, China, 20–23 April 2009, pp 41–48 Yan D, Huang L, Jordan MI (2009) Fast approximate spectral clustering. In: Proceedings of the 15th ACM international conference on knowledge discovery and data mining (SIGKDD’09), Paris, France, June 28–July 01, 2009, pp 907–916 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Applied Informatics Springer Journals

HiVis: a portable, scalable tool for hierarchical visualization and analysis of biological networks

Download PDF
3 pages

Loading next page...
 
/lp/springer-journals/hivis-a-portable-scalable-tool-for-hierarchical-visualization-and-7X9TTn2lDH
Publisher
Springer Journals
Copyright
Copyright © 2018 by The Author(s)
Subject
Computer Science; Computing Methodologies; Bioinformatics; Health Informatics; Computer Imaging, Vision, Pattern Recognition and Graphics; Computer Applications; Statistics for Life Sciences, Medicine, Health Sciences
eISSN
2196-0089
DOI
10.1186/s40535-018-0050-0
Publisher site
See Article on Publisher Site

Abstract

tushikui@sjtu.edu.cn Department of Computer It is very important to analyze the network structure of interacting genes, proteins, Science and Engineering, RNAs, etc. in large-scale biological networks which represent complex biological School of Electronic Information and Electrical systems. Many tools have been made for this purpose. However, they are either unable Engineering, Shanghai to display the hierarchically structured view of the networks or not easy to build in Jiao Tong University, cross-platforms. Here, we present a navigation tool called HiVis for biological network 800 Dongchuan Road, Shanghai 200240, China visualization. HiVis provides a hierarchical view of the networks through a zoom-in or Full list of author information zoom-out function powered by k-means and fast approximate spectral clustering algo- is available at the end of the rithms. It is a cross-platform, portable, fast desktop application to large-scale networks. article Keywords: Hierarchical visualization, Cross-platform, Clustering algorithms Background To the Editor: motivated by HiMap (Shi et al. 2009), we present HiVis, an open-source software that provides hierarchical interactive visualization and analysis for biological networks. It contains three main features: • Not only is it able to visualize networks which contain tens of thousands interactions in a hierarchically structured way, but also it allows the analysis of the local connec- tions centered on a specific element. • It provides a suite of interactive methods for the user to analyze structural detail of the network. • HiVis is a portable cross-platform application, so that users do not need to go through the tedious installation process and bothered by installing a lot of dependent packages. Methods We use a top-down approach to cluster the biological networks into a multi-level node- link graph. We demonstrate the main features in Fig. 1 through a data set from STRING interaction database (https ://strin g-db.org/cgi/input .pl). It is well known that many bio- logical networks contain clique and hub genes which are highly clustered and contain © The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat iveco mmons .org/licen ses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Qiang et al. Appl Inform (2018) 5:3 Page 2 of 3 Fig. 1 Illustration of features in HiVis, a software that provides hierarchical visualization and analysis of biological networks. a The interface of HiVis; b The full scope of the nodes inside the selected cluster in (a); c Displaying the selcted gene, its most related ones and their interactions when choosing a gene in (a); d Displaying the network by a fast approximate spectral clustering method in each hierarchy self-similar structure. Therefore, clustering them together into one node can reveal their hierarchical information and make the visualization readable. Currently, we provide two cluster algorithms, k-means clustering, and fast approxi- mate spectral clustering (Yan et al. 2009), which is faster than normal spectral clustering method and is more suitable for network clustering than k-means algorithm. The idea is to use k-means as a preprocessor and then to perform the normal spectral clustering method. Here, we also implemented a heuristic approach to determine the number of clusters by checking the slope of neighboring points of sorted eigenvalues. Implementation It is difficult to display the biological network meaningfully in one scope, HiVis solves it by cluster them into a hierarchical tree and only reveal the nodes in the current view and the view in the next hierarchy. To be more specific, here, we present an example illus - trated in Fig. 1, 1a is the overview of HiVis, the genes are clustered using k-means, and each node represents a group of them. It can switch the algorithm to modified spectral clustering and the result is shown in Fig.  1d. HiVis offers smooth animation methods to further analyze the computed clusters. When selecting one cluster, it will show a full scope of its inner structure; as shown in Fig.  1b, users can also return to the previous stage, or they can further analyze the current cluster with the same procedure. Apart from that HiVis will show each genes within the cluster, as is shown in the left part of Qiang et al. Appl Inform (2018) 5:3 Page 3 of 3 Fig. 1b, when choosing one gene, HiVis will display the gene and its most related genes in a network, as is shown in Fig. 1c. Thus, it will help to analyze the network locally. Conclusion In this paper, we present HiVis, a software built on electron for hierarchical visualiza- tion and analysis of biological networks. We implemented the k-means clustering, fast approximate spectral clustering algorithm, and force-direct layout algorithm to let HiVis capable of handling large-scale biological data. It is worth noting that this kind of dis- playing technique is very general and can be applied to other networks like social net- work, security network, etc. Authors’ contributions The authors discussed the problem and the solutions were proposed all together. All authors participated in drafting and revising the final manuscript. All authors read and approved the final manuscript. Author details Department of Computer Science and Engineering, School of Electronic Information and Electrical Engineering, Shang- hai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China. Bioinformatics Program, Boston University, Boston 02215, USA. School of Computer Science, Carnegie Mellon University, Pittsburgh 15213, USA. Acknowledgements The work is supported by a starting grant ( WF220403029) from Shanghai Jiao Tong University. Competing interests The authors declare that they have no competing interests. Availability of data and materials The installation package and source code can be accessed at https ://githu b.com/QLigh tman/HiVis . Ethics approval and consent to participate Not applicable. Funding Not applicable. Publisher’s Note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Received: 7 May 2018 Accepted: 31 May 2018 References Protein–protein interaction networks. https ://strin g-db.org/cgi/input .pl Shi L, Cao N, Liu SX, Qian WH, Tan L, Wang GD, Sun JM, Lin CY (2009) HiMap: adaptive visualization of large-scale online social networks. In: Proceedings of IEEE Pacific visualization symposium 2009 (PacificVis’09), Beijing, China, 20–23 April 2009, pp 41–48 Yan D, Huang L, Jordan MI (2009) Fast approximate spectral clustering. In: Proceedings of the 15th ACM international conference on knowledge discovery and data mining (SIGKDD’09), Paris, France, June 28–July 01, 2009, pp 907–916

Journal

Applied Informatics – Springer Journals

Published: Jun 7, 2018

There are no references for this article.