Tutorial - Network Browser

Revision as of 12:25, 21 August 2006 by Smith (talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

Home | Quick Start | Basics | Menu Bar | Preferences | Component Configuration Manager | Workspace | Information Panel | Local Data Files | File Formats | caArray | Array Sets | Marker Sets | Microarray Dataset Viewers | Filtering | Normalization | Tutorial Data | geWorkbench-web Tutorials

Analysis Framework | ANOVA | ARACNe | BLAST | Cellular Networks KnowledgeBase | CeRNA/Hermes Query | Classification (KNN, WV) | Color Mosaic | Consensus Clustering | Cytoscape | Cupid | DeMAND | Expression Value Distribution | Fold-Change | Gene Ontology Term Analysis | Gene Ontology Viewer | GenomeSpace | genSpace | Grid Services | GSEA | Hierarchical Clustering | IDEA | Jmol | K-Means Clustering | LINCS Query | Marker Annotations | MarkUs | Master Regulator Analysis | (MRA-FET Method) | (MRA-MARINa Method) | MatrixREDUCE | MINDy | Pattern Discovery | PCA | Promoter Analysis | Pudge | SAM | Sequence Retriever | SkyBase | SkyLine | SOM | SVM | T-Test | Viper Analysis | Volcano Plot



Outline

Overview

This is a quick introduction to the Network Browser component. This is a beta-release to provide visualizations for adjacency matrices generated by the ARACNE network reverse engineering compoenent and the Interactions component.

Example

  1. Click the Load button and browse to an adjancency file you would like to load.
  2. Push the Draw button.


T NetworkBrowser GUI.png


You will see that the component indicates the number of nodes and edges, but no picture is drawn. This is due to an unresolved problem with Cytoscape integration.

Workaround

You must destroy and then recreate the view.

  1. Under the word Network at upper left, right-click on the file name of the adjacency matrix.
  2. Select Destroy View, as shown below.
  3. Repeat, and Select Create View.


T NetworkBrowser DestroyView.png


After the network has been displayed, improve the layout by selecting Layout->yFiles->Organic:


T NetworkBrowser SetOrganic.png


Afther the layout is applied, the network will appear as follows:

T NetworkBrowser OrganicLayout.png