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Table 1 Tools and resources for visualizing multidimensional cancer genomics data

From: Visualizing multidimensional cancer genomics data

Name Description Visualization type Tool type Data that can be visualized
cBio Cancer Genomics Portal [32]
http://www.cbioportal.org
Resource for visualizing TCGA and other data sets with many features, of which the network viewer and OncoPrint are of special interest. In the network viewer, the portal overlays multidimensional genomics data onto all nodes that are representing genes. This provides the frequency of mutations and copy number alterations (and optionally, mRNA up-/downregulation). OncoPrint shows the same alteration data in a matrix heatmap Networks
Matrix Heatmaps
Web tool Pre-calculated TCGA and other data sets
CircleMap [8]
http://sysbio.soe.ucsc.edu/nets
Tool that produces heatmaps with a circular layout. Different data sets coming from the same samples can be plotted as different layered circles that form a node. The data layers are plotted maintaining the sample order, which can be adjusted by the user Circular heatmaps Command line application
web tool
Any user-prepared data
Circos [24]
http://circos.ca/
Tool for visualizing data and information in a circular layout. It allows intuitive exploration of the relationships between genomic positions, which are depicted as ribbons. Different genomic data types can be represented in different layers of the circle. To a great extent, the color code and plot style for each layer (or data set) can be adjusted by the user Circular genomic coordinates Command line application Any user-prepared data
Caleydo StratomeX [34]http://stratomex.caleydo.org Tool prepared for the visualization of interdependencies between multiple datasets. It allows exploration of relationships between multiple groupings and different datasets. It can cluster genomics data of different alterations and represents them as matrix heatmaps. The different groupings are connected by ribbons whose width corresponds to the number of samples shared by the connected clusters. Clinical data and pathway maps can be integrated to characterize the clusters Matrix heatmap with option to visualize pathway maps Desktop application (Java) Any user-prepared data (matrices, clusterings). Prepared TCGA data available at http://compbio.med.harvard.edu/tcga/stratomex
Cytoscape [36]http://www.cytoscape.org Software for visualizing complex networks and integrating these with any type of attribute data such as genomics data and clinical patient information. An extensive library of community-developed plugins is available, some of which (for example, Reactome FIs) focus on cancer data analysis [38] Networks Desktop application (Java) The stand-alone application supports any user-prepared network or attribute data. Additional data are available via various plugins (for example, GeneMANIA [72] for networks)
Genomica [73] http://genomica.weizmann.ac.il Tool that can be used to analyze and visualize genomic data. Data can be visualized as heatmaps or along genomic coordinates. Module maps and module networks can be created from expression data and can integrate gene expression data, DNA sequence data, and gene and experiment annotations Matrix heatmap Genomic coordinates Desktop application (Java) User-prepared data
Gitools [31]
http://www.gitools.org
Tool for analysis and visualization of genomic data using interactive heatmaps. It allows loading of multidimensional matrices (with several values per cell), and thus is very well suited for the visualization and exploration of multidimensional cancer genomics data. It contains several analyses and options that are specifically designed for the exploration of cancer genomics data Matrix heatmap with interactive features Desktop application (Java) Any user-prepared data and data imported from IntOGen [33] database, as well as any Biomart [69, 73] database
Integrative Genomics Viewer (IGV) [20]http://www.broadinstitute.org/igv Visualization tool for interactive exploration of integrated genomics datasets, with a focus on good performance when working with large data sets. All tracks can be annotated with color-coded sample and clinical information; genomic regions can be annotated with text labels. All of the common genomic file formats are supported, including array-based data, next-generation sequence data formats and genomic annotations Genomic coordinates Desktop application (Java) User-prepared data and data from the IGV server, including some TCGA data. In addition, IGV can be accessed from external tools such as GenePattern [68]
IntOGen [33]
http://beta.intogen.org
Resource that is used to analyze and visualize cancer genomics data, including expression, copy number variation and somatic mutation data from cancer genomic projects. Various visualization options are offered, of which web-interactive heatmaps (using jheatmap [74]) are of special interest. These are used to display alterations per gene in a cohort of tumor samples or in a set of tumor types Matrix heatmaps with interactive features Web tool Pre-calculated data from more than 300 cancer genomic experiments and user-prepared data for somatic mutations in tumors
NAViGaTOR [75]http://ophid.utoronto.ca/navigator Tool for visualizing and analyzing protein-protein interaction networks (Network Analysis, Visualization and Graphing TORonto). The network visualization options can be customized to represent genomic data properties by automatically mapping attribute values to visual properties Networks Desktop application (Java) User-prepared data. Data can also be loaded via plugins from multiple portals (such as Reactome [76] or KEGG [77])
Regulome Explorer [70]http://explorer.cancerregulome.org Tool for the integrative exploration of associations between clinical and molecular features of data from the TCGA project. The visualization is interactive and the displayed data can be filtered according to different criteria. Visualization options include circular and linear genomic coordinates and networks Circular and linear genomic coordinates
Networks
Web tool Pre-calculated TCGA data
Savant Genome Browser [22]http://genomesavant.com/savant Desktop visualization and analysis browser for genomics data. This tool was primarily developed for the effective visualization of large sets of high-throughput sequencing data, similar to IGV. Multiple visualization modes enable the exploration of genome-based sequence, points, intervals, or continuous datasets. Plugins are available, amongst which is the WikiPathways [78] plugin, which aids the navigation of the data by the integration of pathways Genomic coordinates Desktop application (Java) User-prepared data or data that can be downloaded through plugins such as the USCS Explorer plugin
The Cancer Genome Workbench (CGWB) [79]
https://cgwb.nci.nih.gov/
Host for mutation, copy number, expression, and methylation data from a number of projects. It has tools for visualizing sample-level genomic and transcription alterations in various cancers. The main viewers in CGWB are Integrated tracks view, Heatmap view and Bambino, an alignment viewer. The interface of CGWB is based on the UCSC Genome Browser [80] Genomic coordinates
Heatmap
Web tool Pre-calculated data from various resources (such as Cosmic, NCI-60 and TCGA [40, 65, 81])
The user can also add custom data tracks for visualization
UCSC Cancer Genomics Browser [21]
https://genome-cancer.ucsc.edu
Tool for hosting, visualizing, and analyzing cancer genomics datasets. The browser can display genome-wide experimental measurements for multiple samples, which can originate from multiple data sets alongside their associated color-coded clinical information. The browser provides interactive views of data from genomic regions to annotated biological pathways and user-contributed collections of genes. Integrated statistical tools provide quantitative analysis within all available datasets Genomic coordinates
Heatmap
Web tool TCGA data and data from independent publications available from the UCSC server. In addition to open access to public datasets, the browser provides controlled access to private project data