Visualization Of Clustering Results Research Articles

Recursive Consensus Clustering for novel subtype discovery from transcriptome data

Large-scale transcriptomic data is used by biologists for the discovery of new molecular patterns or cell subpopulations. Clustering is one of the most popular methods for dimensionality reduction and data analysis for large scale datasets. The major problem while clustering the data is the selection of the optimal number of clusters (k) for each dataset and to discover new insights from it. We have developed Recursive Consensus Clustering (RCC), an unsupervised clustering algorithm for novel subtype discovery from both bulk and single-cell datasets. RCC is available as an R package and facilitates the generation of new biological insights through intuitive visualization of clustering results.

CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks.

Nowadays, cluster analysis of biological networks has become one of the most important approaches to identifying functional modules as well as predicting protein complexes and network biomarkers. Furthermore, the visualization of clustering results is crucial to display the structure of biological networks. Here we present CytoCluster, a cytoscape plugin integrating six clustering algorithms, HC-PIN (Hierarchical Clustering algorithm in Protein Interaction Networks), OH-PIN (identifying Overlapping and Hierarchical modules in Protein Interaction Networks), IPCA (Identifying Protein Complex Algorithm), ClusterONE (Clustering with Overlapping Neighborhood Expansion), DCU (Detecting Complexes based on Uncertain graph model), IPC-MCE (Identifying Protein Complexes based on Maximal Complex Extension), and BinGO (the Biological networks Gene Ontology) function. Users can select different clustering algorithms according to their requirements. The main function of these six clustering algorithms is to detect protein complexes or functional modules. In addition, BinGO is used to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. CytoCluster can be easily expanded, so that more clustering algorithms and functions can be added to this plugin. Since it was created in July 2013, CytoCluster has been downloaded more than 9700 times in the Cytoscape App store and has already been applied to the analysis of different biological networks. CytoCluster is available from http://apps.cytoscape.org/apps/cytocluster.

K-means Parallelization Algorithm Based on MapReduce

Spatial Cluster analysis is another important technique in the field of spatial data mining, especially the K-Means spatial clustering method, which can deal with spatial objects with geographical location and attribute. However, with the development of the information society, the spatial data grows explosively, but the serial algorithm has low computing efficiency and is difficult to process massive spatial data. Aiming at spatial with a double meaning of location and attribute, the paper designed and implemented KMeans spatial clustering parallel algorithm on Hadoop. Using Yahoo Weibo user data is to do clustering analysis. Finally, the visualization of clustering results was implemented by Google Map.

ClusterViz: A Cytoscape APP for Cluster Analysis of Biological Network

Cluster analysis of biological networks is one of the most important approaches for identifying functional modules and predicting protein functions. Furthermore, visualization of clustering results is crucial to uncover the structure of biological networks. In this paper, ClusterViz, an APP of Cytoscape 3 for cluster analysis and visualization, has been developed. In order to reduce complexity and enable extendibility for ClusterViz, we designed the architecture of ClusterViz based on the framework of Open Services Gateway Initiative. According to the architecture, the implementation of ClusterViz is partitioned into three modules including interface of ClusterViz, clustering algorithms and visualization and export. ClusterViz fascinates the comparison of the results of different algorithms to do further related analysis. Three commonly used clustering algorithms, FAG-EC, EAGLE and MCODE, are included in the current version. Due to adopting the abstract interface of algorithms in module of the clustering algorithms, more clustering algorithms can be included for the future use. To illustrate usability of ClusterViz, we provided three examples with detailed steps from the important scientific articles, which show that our tool has helped several research teams do their research work on the mechanism of the biological networks.

A Novel Method for Visualization of Clustering Results

Sammon mapping is an approach of nonlinear dimension reduction and can be used for visualization. To avoid numerical complexity of the algorithm of traditional Sammon mapping, Kovacs and Abonyi (2004) proposed a modified Sammon mapping method. However, this improvement can only be applied to fuzzy clustering results. By using the property of Fermat point, we develop a new method in this article that can be applied to any clustering results. Different from other methods of visualization, we transfer information of clustering results into concentric circles around the Fermat points. So our procedure can demonstrate the data structure in a more informative way and the clustering results become easier to understand, especially for nonprofessionals. The effectiveness of the proposed method is studied by application to a real data in this article.