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

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Onto-Compare Help

Using Onto-Compare


Tree View Results
Table View Results
Operational Features

More Features


Onto-Compare is a tool that allows efficient comparisons of any set of commercial or custom arrays. Using Onto-Compare, a researcher can determine quickly which array or set of arrays, covers best the hypotheses-studied.

Using Onto-Compare (top)

Once the user is logged in, she will be presented with an HTML page and a pop-up, as shown in Fig. 1A. The user can proceed further by click on  or .


Figure 1A: Request for Granting the session.

Figure 1B: Onto-Tools chooser frame.

The user will then see Onto-tools chooser frame as shown in Figure 1B. The user can check a radio button, corresponding to a particular tool and click to use that particular tool.

On checking the Onto-Compare (OC) check box and clicking , starts Onto-Compare and the user see the Onto-Compare Input form as shown in figure 2A-2B.


            Figure 2A: Onto-Compare Main                                                  Figure 2B: Onto-Compare three level tree (Expanded)

Onto-Compare allows the user to compare the functional bias of two or more arrays. The user can selects the arrays of her interest from the OC tree. The tree is first organized by manufacturers. The arrays are then organized by their respective organisms. The tree can be traversed by expanding or collapsing a combination of nodes at different levels of the tree. The user can expand or collapse a particular node by clicking the handle image to the left of that node. The user can select an array by traversing the tree to the particular array and checking the box to its left.

The user can upload a custom chip of her own by submitting a file containing the list of genes, one gene per line. To submit the input file, the user clicks the button next to "Input 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.

Note: There are some constraints on the format of input file. The input file must be a simple ASCII file ( i.e. the input file should be prepared in an ASCII text editor such as notepad on windows platform or gedit, pico or vi  on various UNIX platforms, but not in MS-Word, MS-Excel, Star Office or Open Office that creates a binary file). The file can contain either accession numbers, cluster identifiers or probe identifiers but not a combination of them. Each identifier should be listed on a separate line. 

The user has to specify the type of input by checking an appropriate radio button. To specify organism corresponding to the custom chip, the user can select a specific organism from the drop down menu.

 The user starts the comparison by clicking the button. This will open up a pre-results page. The user can know the time elapsed since the submission of the request. Below the time elapsed message is the message which informs the user about the stage of processing of her request.

Figure 3: Onto-Compare Pre Results Page

Results (top)

Figure 4: Onto-Compare Results

Display of Onto-Compare (OC) results is now provided into two views: 1. Tree View 2. Table View.

Tree view displays the results in a tree structure that represents the structure of ontology from Gene Ontology (GO) Consortium. The conventional Table display is in Table View.

Tree View Results (top)

The Tree View initially displays the 2 level tree. A user can expand or collapse any node in the tree by clicking the handle-like icon next to each term. The Tree View gives the corresponding position of the ontology term in the GO Tree and the number of genes corresponding to each input array.

Note: All the buttons are disabled in Tree View. 

Figure 5: Tree View


Table View Results (top)

The first column of the result table displays the ontology terms and chromosome names. Each of rest of the columns correspond to one of the input arrays. They will be referred to array columns for rest of the discussion. The array columns are in "integer[integer]" format. The first integer represents the total number of unique accession numbers on the corresponding array for a given ontology term. The integer in square bracket represents the total number of unique UniGene cluster IDs for the given ontology term.

Figure 6: Table View


Operational Features (top)

The user can select a particular ontology term by checking the check box to the left of the corresponding ontology term. The user can select particular array by checking the check box besides the the corresponding array.

The user can view a particular functional category in Table View by selecting one from the Drop Down list. The default is Biological Process.

The user may want to see combination of two or more arrays. The user needs to select 2 or more arrays. After selecting the arrays on clicking button the user will be able to see the combination of both the arrays. The two arrays will be represented in a single column in both the views. Figure 7 shows the effect of this button in Table View.

Figure 7: Merged Arrays


- The user may want to concentrate on particular set of functions instead of all the functions of the array. The user need to select the functions he/she is interested in by checking in the box besides the name of the function. User can select as many functions as he/she wants. After selecting the functions user clicks on this button and the sample output is as follows. The output will only show the selected function in Table View.

Note: works only on Table View.

- The user may want to have the results emailed to his/her email address. The click of this button will email the results to user's account.


More Features (top)

The user may want to know more details of a particular function in a particular array for better analysis. The user can ask for more details for each function under each array by clicking the hyper linked number of sequences. This will send a request to the server for more details and the server responds with a HTML page that contains list of Probe IDs, Accession ID, Cluster ID, Locus ID and Gene. 

Figure 8: Hyper linked number of sequence


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