1OmicsViz: Tutorial and usage 1. Introduction OmicsViz is a Cytoscape plugin (cytoscape2.4 and 2.5) dedicated to providing useful visualization and an integrated analysis tool for large-scale omics data. OmicsViz imports omics data into Cytoscape and visualizes it on a graph according to the change of gene experimental values (Figure 1). OmicsViz also provides a mapping function between two different species or between probe set and experimental names and node names in a network. For example, when you load an Arabidopsis metabolic pathway in Cytoscape and you have a Grape gene expression file, OmicsViz can associate the file with the Arabidopsis pathway based on gene mapping file which contains orthologous genes between the two species. Figure 1 Overview of the OmicsViz tool windows. 1.1 Structure of this Document Section 1. Information on getting started with the plugin and tutorial. Section 2. Tutorial for loading expression data from the same species and across species. Section 3. Tutorial on loading and view metabolomics data. (not complete) Section 4. Information on data file formats for loading your own data with the OmicsViz plugin. 1.2 Loading the OmicsViz Plugin Before starting the tutorial, please make sure that you have downloaded and installed a current version of Cytoscape (2.4 or higher) on your computer. Next, download the OmicsViz plugin from the MetNet for Cytoscape plugin page. Put the file, OmicsViz1.x.jar, into the folder called plugins in the Cytoscape directory2on your computer. The directory on a Windows computer is shown in Figure 2. Figure 2 Location of the plugins and sampleData folders in the Cytoscape application. 1.3 Loading the OmicsViz Sample Data Files Before starting the tutorial, please make sure that you have downloaded and installed the OmicsViz sample data files from the MetNet plugin page. Unzip the file, OmicsVizsampledata.zip, into the folder called sampleData in the Cytoscape directory on your computer. The sampleData directory on a Windows computer is shown in Figure 2. The contents of the OmicsViz sample data file are listed in Table I. The tutorial assumes that the MetNet Sample data is in the Cytoscape sampleData folder. Once the plugin and data have been added to the proper folders, open the Cytoscape application. Table I. Contents of the OmicsViz sample data folder File Name File Type Description Acetyl-CoAbiotin.cys Cytoscape session file Acetyl-CoAbiotin pathway with Acetyl-CoAbiotinwithATexp.cys Cytoscape session file Acetyl-CoAbiotin pathway with expression data attached for Omics Vis tutorials. Expression_AT4rmameans.txt Expression Data A sample gene expression data file of Arabidopsis from Plexdb.org. VV4_mean.txt Expression Data A sample gene expression data file of Vitis vinifera from Plexdb.org. Mapping_AtProbesToAtLoci.txt Mapping file A sample mapping file which maps between Arabidopsis Locus ID and Arabidopsis Probe ID Mapping_VVProbestoATLoci.txt Mapping file A sample mapping file which maps between Arabidopsis Locus ID and Grape Probe ID MetabolitesMetMole.txt Mapping file A mapping file from MetNet ID to Metabolite ID in experiment. Experiment EIE2.txt Metabolomics data file. A sample metabolomics experiment data set from Arabidopsis, available from www.plantmetabolomics.org3 2. Tutorial for Viewing Expression Data 1. Complete the instructions in sections 1.2 and 1.3 above before starting the tutorial to make sure that the plugin and sample data are properly installed. The tutorial assumes that the MetNet Sample data are in the Cytoscape sampleData folder. 2. Open the Cytoscape session file, Acetyl-CoAbiotin.cys by selecting File-> Open on the top Cytoscape menu and selecting the file. This session file contains a pathway file and an associated visual mapping file. Your screen should look like Figure 3. Figure 3. Cytoscape window upon opening the Acetyl-CoAbiotin.cys file. This session file contains pathway data, visual attributes for the graph, and graph layout information. Clicking on the tab labeled VizMapper in the Control Panel will allow exploration of the node colors.4 If you are not familiar with Cytoscape, explore the network by zooming in using the magnifying glass icon. Also, try selecting alternative graph layouts on the Layout menu at the top. For more details on the basic use of Cytoscape, please look at the online tutorials available at the Cytoscape website. Information about individual nodes can be listed in the Data Panel in the lower right hand corner of the Cytoscape window. Right clicking on the icon circled in red in Figure 3 allows the user to select what node attributes can be seen. For this tutorial, right click on the icon and select the location, nodeType, and show boxes. This gives information about the subcellular location, the role of the node, and the name of the node. Try highlighting a few nodes (they will turn pink) and looking at the information as shown in Figure 4. Important note: Network data from different sources will have different attributes and names. This information only holds for data from the MetNet Arabidopsis pathway database. Figure 4. Information about the selected nodes, highlighted in pink, is displayed in the Data Panel in the lower left corner.5 3. Go to the Plugins Menu in Cytoscape and select the OmicsViz option. Choose the “Select Type of Experiment Data File” option menu and select the Gene Expression Data option. Other options are Metabolomics Data or other types of experimental data. Next, choose the “Name the MappingID for Data File” option and select the Arabidopsis ProbeSet option. This option allows the attribute mapping information to be labeled with a user specified ID. Figure 5. OmicsViz plugin Window64 The next step is selecting the input experiment data file. Click on the select button circled in Figure 6 and browse the sampleData folder to find the experimental data file, Expression_AT4rmameans.txt. Data files can be in the form of a tabbed text file or an excel spreadsheet where each row of the file is a set of measurements of a probeset or compound and each column is a hybridization or condition. The resulting window can be seen in Figure 6. OmicsViz window before file selection Figure 7. OmicsViz after the Experiment data file is selected. The ellipse highlights the next step of selecting the mapping file.7 5. Select the mapping file that maps Arabidopsis probe sets to