413 State Hall, Department of Computer Science, Wayne State University, Detroit MI 48202
Phone: (313) 577-5070 Fax: (313) 577-6868

Link to Dr. Sorin Draghici's home page

 

Onto-Design Help

Using Onto-Design

GO Tree Input
File Input

Results

Reading the Results
Operational Features

 

Onto-Design is a tool that allows the user to select genes that represent given functional categories.

Using Onto-Design (top)

After logging on the Onto-Tools site, click on "Onto-Design" tab to use Onto-Design (OD). Onto-Design allows the user to compare the functions on the basis of the cluster id's they are present in. Input to OD is a list of ontology terms. A user can either select a term by browsing the GO Tree or can submit a file containing the terms one per line

Figure 1: Onto-Design Main 

 

GO Tree Input (top)

The user clicks on the handle-like button next to each node in the tree to expand or collapse the tree. Clicking a left mouse button on a node toggles the node state between checked and unchecked. Clicking a right mouse button on a node displays a pop up menu. Selecting "Expand current node" in the pop up menu, expands the current node completely. If any of the child node of the current node has its own children, they are also expanded. Selecting "Collapse current node" collapses the current node as well as all of its children nodes. Clicking on "Select children of current node" carries out two operations: first, it expands the current node completely (same as the expand current node) and two, it selects all of the nodes for an array design. Clicking on "Deselect children of current node" only deselects the current node and all of its children. It does not collapse the current node entirely. After selecting the ontology terms of interests, the user selects the organism and clicks the button.

Figure 2: GO Tree and Pop Up menu

File Input (top)

The user can also submit his own list of function names through a file. To submit the input file, the user clicks the button next to "Attach your file". Clicking the button opens up a file dialog box that displays a list of files on the user's computer. The user navigates to the required directory and selects an appropriate input file. After selecting the file, the user clicks the button in the file dialog box.

The user needs to specify the organism by selecting from the drop down list besides "Select Organism".  The user can view the mutually exclusive set of cluster ids that correspond to each function uniquely from the input by selecting the "Unique to Function" option. The user needs to click the button to run Onto-Design. 

Results (top)

Figure 3: Onto-Design Results

 

Understanding the Results (top)

The results are displayed in another window as a two-column table. The first column is the ontology term itself and the second column displays a list of all the UniGene cluster IDs of the given organism found for the given term. Total number of cluster IDs found for a term are displayed next to the term itself.

Each Cluster Id is hyper-linked. The user can ask for more details for each Cluster ID by clicking on the hyper link. This will send a request to the server for more details and the server responds with a HTML page that contains list of Locus Link, Gene, Gene Title, and list of Accession ID. The Locus Link and the each accession id in the list is hyper-linked to the corresponding section of  NCBI.

Figure 4: Cluster Id Details

 

Operational Features (top)

The user may wish to customize the array in various ways. For example, the user may be interested in studying a hypothesis in which more than one biological processes are known to occur simultaneously. In such conditions, the user will want to design an array with genes that are involved in all of the biological processes or in as many as possible. In conditions such as this, the user selects the ontology terms of interest by clicking the check box next to the term, select the "intersection" radio button and then click the button. The result of this operation is the list of genes that are annotated using all of the selected terms. In other words, the result is the intersection of the individual list of UniGene IDs of each of the selected terms.

If the intersection of the terms shows that there are not many genes common between the selected terms, the user may wish to have all the genes on the array that are annotated using any of the selected terms. In such a conditions, after selecting the terms of interest, the user selects the "union" radio button and clicks the button. The result is the union of the each individual list of UniGene IDs. 

Another interesting condition can be when two or more biological processes are known to be regulated simultaneously and the user is only interested in studying one of them. In this condition, the user will like to fabricate a microarray with genes that are only involved in the biological process of the interest and not in the other biological process. In such a condition the user first clicks the "difference" radio button, then selects the biological process of the interest from the first drop down list of the terms. Next the user selects the biological process whose genes he/she wants to be excluded and clicks the button. The result is a list of genes that are only known to be involved in the biological process of the interest. 

The user can fine tune the array design by repeatedly carrying out the union, intersection and difference steps.

The button is similar to difference operation except that it works on all of the terms instead of the selected terms. button resets the table to the original results and hence removes all of the operations carried out by the user.

The user can also have the results emailed to his account by clicking the button.


Contact us : Dr. Sorin Draghici   -
               or Purvesh Khatri        -

 

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copyright 2003 Intelligent Systems and Bioinformatics Laboratory, Computer Science Department, Wayne State University