Gene Ontology Viewer
|
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 |
Contents
Overview
The Gene Ontology Analysis Viewer allows direct browsing of the Gene Ontology, and also the visualization of GO Term analysis results.
The viewer presents the GO both in tabular form (Table tab) as well as in a tree form (Tree tab).
In addition, three windows provide additional details:
- A list below the selection windows shows all genes annotated with a selected term.
- The "Single Term View" shows the complete tree, including multiple paths through the GO directed acyclic graph, for any selected term.
- The Term/Gene Details windows provides additional details on an term or gene selected in the GO browser or the gene list.
Standalone Viewer Details
Table Browser
GO Subontology (Namespaces) - radio buttons allow the user to view all three subontologies, or just one at a time. The choices are:
- All
- Molecular Function (M)
- Biological Process (B)
- Cellular Component (C)
- All
Table Columns
- GO:ID - The Gene Ontology Term ID
- Name: The name associated with the GO Term.
- Namespace - the Gene Ontology Namespace to which each GO term belongs, abbreviated as as shown above under Subontology
Tree Browser
Browse
The Viewer also allows the Gene Ontology to be directly browsed in tree format. Clicking on the arrow in front of any term will open that term to display its child terms, until a final leaf node is reached. The first picture below shows the tree with just the three top level subontologies displayed.
Search by GO term ID or name
The Tree Browser allows terms to be searched either by ID or by name. Enter the desired search term and hit "Search". Here, term 3700 has been searched for. Term details are displayed in the other three windows.
Gene List
Term/Gene Details
