Difference between revisions of "GO Graphic Viewer"
m (→Contact) |
m |
||
| Line 1: | Line 1: | ||
| − | + | {{TocRight}} | |
| − | + | ||
The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the result from the GO::TermFinder Perl module created by the [http://genome-www5.stanford.edu/ Stanford Microarray Database (SMD)]. This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process. This distribution also includes two examples of its use in Web-based user interfaces (goView.pl and goTermFinder.pl). It is a component of the Generic Model Organism Systems Database project. | The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the result from the GO::TermFinder Perl module created by the [http://genome-www5.stanford.edu/ Stanford Microarray Database (SMD)]. This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process. This distribution also includes two examples of its use in Web-based user interfaces (goView.pl and goTermFinder.pl). It is a component of the Generic Model Organism Systems Database project. | ||
| Line 24: | Line 23: | ||
From the README: | From the README: | ||
| − | The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that | + | The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that |
| − | displays the parent and child relationships of a selected GO term. Two | + | displays the parent and child relationships of a selected GO term. Two |
| − | examples of its use in web-based user interfaces are included, goView.pl and | + | examples of its use in web-based user interfaces are included, goView.pl and |
| − | goTermFinder.pl. | + | goTermFinder.pl. |
| − | The goView.pl program uses the Bio::GMOD::GO::View module to create a | + | The goView.pl program uses the Bio::GMOD::GO::View module to create a |
| − | web-based user interface that can be used to view and browse the Gene Ontology. | + | web-based user interface that can be used to view and browse the Gene Ontology. |
| − | The terms are color coded based on whether they have child terms. A blue box | + | The terms are color coded based on whether they have child terms. A blue box |
| − | indicates that the term has child terms while a gray box indicates that the term | + | indicates that the term has child terms while a gray box indicates that the term |
| − | does not have child terms. Clicking on a blue box will expand that branch of the | + | does not have child terms. Clicking on a blue box will expand that branch of the |
ontology. The blue up arrow indicates that there are additional parent terms | ontology. The blue up arrow indicates that there are additional parent terms | ||
| − | available for the selected GO term. Clicking on the up arrow will display the | + | available for the selected GO term. Clicking on the up arrow will display the |
parents of the selected GO term. | parents of the selected GO term. | ||
| − | The goTermFinder.pl program combines the Bio::GMOD::GO::View module with the | + | The goTermFinder.pl program combines the Bio::GMOD::GO::View module with the |
| − | GO::TermFinder module to create a user-friendly resource for analyzing and viewing | + | GO::TermFinder module to create a user-friendly resource for analyzing and viewing |
| − | GO terms that are shared by a group of genes. The Bio::GMOD::GO::View will display | + | GO terms that are shared by a group of genes. The Bio::GMOD::GO::View will display |
| − | the ontology based on the GO terms that are common among a group of genes (as | + | the ontology based on the GO terms that are common among a group of genes (as |
| − | determined by the GO::TermFinder module). The boxes will be color-coded to indicate | + | determined by the GO::TermFinder module). The boxes will be color-coded to indicate |
| − | how significant a GO term is as a parent for a given group of genes. In addition, | + | how significant a GO term is as a parent for a given group of genes. In addition, |
| − | GO terms from the gene-association files that cannot be found in the ontology files | + | GO terms from the gene-association files that cannot be found in the ontology files |
will be displayed at the top of the graphic. | will be displayed at the top of the graphic. | ||
| − | This distribution includes the Bio::GMOD::GO::View module, an example of the | + | This distribution includes the Bio::GMOD::GO::View module, an example of the |
| − | Bio::GMOD::GO::View module used in a web-based interface (goView.pl), and the | + | Bio::GMOD::GO::View module used in a web-based interface (goView.pl), and the |
| − | Bio::GMOD::GO::View module as a web-based interface in conjunction with the | + | Bio::GMOD::GO::View module as a web-based interface in conjunction with the |
| − | GO::TermFinder (goTermFinder.pl). | + | GO::TermFinder (goTermFinder.pl). |
Revision as of 17:31, 20 October 2009
The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. It also provides the visualization for the result from the GO::TermFinder Perl module created by the Stanford Microarray Database (SMD). This module is useful when analyzing experimental or computational results that produce a set of gene products that may have a common function or process. This distribution also includes two examples of its use in Web-based user interfaces (goView.pl and goTermFinder.pl). It is a component of the Generic Model Organism Systems Database project.
Demo & Screenshots
Requirements
- The Apache web server (http://www.apache.org/)
- Perl 5.005 or higher
- GD
- CGI
- GraphViz
- GO::TermFinder
- Bioperl
Documentation
From the README:
The GO Graphic Viewer module (Bio::GMOD::GO::View) generates a graphic that displays the parent and child relationships of a selected GO term. Two examples of its use in web-based user interfaces are included, goView.pl and goTermFinder.pl.
The goView.pl program uses the Bio::GMOD::GO::View module to create a web-based user interface that can be used to view and browse the Gene Ontology. The terms are color coded based on whether they have child terms. A blue box indicates that the term has child terms while a gray box indicates that the term does not have child terms. Clicking on a blue box will expand that branch of the ontology. The blue up arrow indicates that there are additional parent terms available for the selected GO term. Clicking on the up arrow will display the parents of the selected GO term.
The goTermFinder.pl program combines the Bio::GMOD::GO::View module with the GO::TermFinder module to create a user-friendly resource for analyzing and viewing GO terms that are shared by a group of genes. The Bio::GMOD::GO::View will display the ontology based on the GO terms that are common among a group of genes (as determined by the GO::TermFinder module). The boxes will be color-coded to indicate how significant a GO term is as a parent for a given group of genes. In addition, GO terms from the gene-association files that cannot be found in the ontology files will be displayed at the top of the graphic.
This distribution includes the Bio::GMOD::GO::View module, an example of the Bio::GMOD::GO::View module used in a web-based interface (goView.pl), and the Bio::GMOD::GO::View module as a web-based interface in conjunction with the GO::TermFinder (goTermFinder.pl).
