GenMAPP-CS User Manual
Introduction
GenMAPP-CS is open-source software for pathway visualization and analysis, bringing the intuitive and easy-to-use features of GenMAPP to the powerful and flexible Cytoscape platform. This manual describes the use of GenMAPP-CS. For details on Cytoscape functionality and usage, refer to the Cytoscape manual.
Installing GenMAPP-CS
GenMAPP-CS beta is now available for testing only.
GenMAPP-CS overview

While GenMAPP-CS "lives" in the Cytoscape environment and therefor shares many interface components with Cytoscape, it also has a set of GenMAPP-specific components that correlate with the main object types in GenMAPP-CS:

  • Database: A database contains species-specific identifier mappings. Most commonly, the GenMAPP-CS databases are Derby databases generated from Ensembl, either accessed locally or through BridgeDb web serbvices. GenMAPP database resources are configurable, including using a user-defined local or remote file.
  • Network: A network is a set of connected nodes. For example, a network can be a biological pathway, the nodes are biological entities like genes, gene products, metabolites and references to other pathways.
  • Dataset: A dataset is a set of values associated with biological entities (nodes). For example, a dataset can be experimental data from a microarray experiment, with the probes on the array being the biological entities.
  • Criteria set: A criteria set is one or more logical rules for one or more data columns of a dataset. A criteria is also associated with a color. Criteria are evaluated for all biological entities in networks that are mapped to the relevant data, and genes, gene products and metabolites are colored accordingly.
Network view window
The Network View Window displays a network and is located in the center of the GenMAPP-CS interface. If multiple networks are loaded there will be one network view window per network.
Workspace panel
The Workspace panel is located in the left side panel. It provides immediate access to all the main features of GenMAPP-CS. The panel defines the major object types and actions supported by GenMAPP-CS, including datasets, criteria sets and networks. The Workspace panel consists of 6 distinct sections: Database, Actions, Network, Dataset, Criteria Set and Results.
Database
The Database panel contains a drop-down menu for selecting the species of interest. The species list is based on available BridgeDb resources. GenMAPP database resources are also configurable. Clicking the Manually configure database resources button brings up the configuration interface. ID Mapping
  • To add a local Derby database, click on Databases in the left-side panel and select a local Derby database (.bridge/.pgdb).
  • To add web service based identifier mapping, click on Web Services in the left side-panel. Available web service resources include BridgeDb (default), BioMart, PICR, Synergizer and CRONOS.
  • To select any other file (local or remote) for identifier mapping, click on Local/Remote Files in the left side-panel.
File-based ID Mapping
  1. Under Data Source, select either Local or Remote/URL depending on the file type. If it's a remote file, enter the URL and click Select.
  2. Under Show advanced option you can specify the delimiters used in the file. You can also select to use transitivity for ID mappings, meaning if A links to B and A links to C, transitive mapping also links B to C.
  3. If the file preview looks as expected, click OK to continue.
For advanced identifer mapping options, use CyThesaurus.
Actions
The Actions panel of the Workspace panel contains a drop-down menu with the most common GenMAPP actions. Some actions have prerequisites and will therefore appear as inactive (grey) in the list until prerequisites are met. Below is a full list of available actions. The list of actions in the drop-down can also be customized.
  • Open session file: Opens a session file, which can contain one or more networks with mapped data.
  • Open network file: Opens a network file in any Cytoscape-compatible network format.
  • Load network from web: Loads networks from public network databases.
  • Import dataset from table: Imports data in the form of a spreadsheet table with one or more columns of data.
  • Create new criteria set: Access to Criteria Mapper interface for creating Criteria Sets.
  • Run clusterMaker: Cluster analysis of data and/or networks with clusterMaker.
  • Run GO-Elite: Pathway and GO over-representation analysis with GO-Elite.
  • Export image: Export pathways in multiple image formats, including PDF, SVG, EPS, JPEG, PNG and BMP.
Configuring the Actions list

The Actions list can be configured to include additional items, multiple instances of the same item and can also be configured as a workflow environment. Clicking the Manually configure action list button brings up the configuration interface.

Configure Action List

Currently selected actions that will appear in the drop-down are shown under Selected actions and all available actions are listed under Available actions.

  1. To add an action to this list, select it from the Available actions list and click the right arrow button. Likewise to remove an action from the list, select it under Selected actions and click the left arrow.
  2. It is possible to have GenMAPP step through all actions in the final list by selecting the Automatically step through actions check-box. This options creates a workflow environment where the next action on the list is selected once the previous one is completed.
Note that any changes made to the default Actions menu will NOT be saved between sessions.
Network
The Network section of the Workspace panel is the GenMAPP-CS network manager. It displays the pathway name, number of nodes and edges, and the view state (red/green highlight). Network selection is indicated by a blue background. Each network has context menu.
Dataset
The Dataset panel of the Workspace panel lists data files loaded through the GenMAPP-CS data import. The name and number of rows from each data file are displayed. By default, all data files loaded through this mechanism are automatically mapped to all existing and subsequently loaded networks and pathways. Automatic mapping can be manually disabled per dataset and the green or red highlight will indicate whether a given dataset is attached and ready to be mapped.
Criteria Set
The Criteria Set panel of the Workspace panel lists any criteria set created with Criteria Mapper. The number of criteria in each criteria set (Criteria) and the number of nodes in the data set matching the criteria in loaded networks (Nodes) are displayed. Criteria set are automatically applied to new networks. The highlighting of the criteria set displays whether a criteria set is applied to the current set of pathways (green) or not (red).
Results
The Results panel of the Workspace panel lists any analysis results or ongoing analysis sesssions. Clicking on a specific entry in the results section will bring up the corresponding analysis results (or status of ongoing analysis) in the Results panel. The highlighting of results indicates whether the corresponding analysis is complete (green) or ongoing (red).

Data Panel
The Data Panel displays any data associated with selected nodes in the network. The display of columns in the Data panel is customizable, and individual data values are editable through this interface.
Results Panel
The Results Panel contains multiple tabs and can display either analysis results (or analysis status) from GO-Elite, or the Backpage for a selected node in the network. The Backpage displays detailed information about the selected node, such as identifier assignment, links to other databases and a summary of any data loaded for that node.