BioIntepreter Help File

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Biointerpreter User Manual

NOTE: 75% of the microarray data is not avilable in Demo version. Subscribe to the Full version and get other advantages.

Biointerpreter is an online tool with user friendly web interface. There is no special training required to efficiently use the tool. Fill up the registration form to obtain a or Demo Login purchase subscription. Visit http://www.genotypic.co.in/bionterpreter_login.htm to reach login page.

Login Page

Your email ID is the LoginID (not case sencitive), the password is case sensitive. If the server is busy with other requests it will take up 10 seconds for logging into the program. If the login check internet connection by visiting other sites. If you can reach other websites, try logging again. Try logging into the Demo server if the login fails repeatedly. If you are using a Demo login, verify if you have exceeded the number of logins or the demo period is completed. Email biointerpreter@genotypic.co.in to obtain a new demo login or purchase a subscription.

Biointerpreter Query page

Paste the Gene Ids into the text box as shown below. The Ids should be separated by carriage return i.e. each ID should be in a separate line. Example Gene ids

1. Type the study name in the box provided. (Study name is for your reference, it does not change the way program works.)

2. Choose the P value cutoff (choose default value of 0.05 if you are doing the search for the first search)

3. Click on the Search button.

The search time taken is 10 seconds to 30 seconds and might vary depending on the number of IDs entered and the internet speed. Reduce the number of Ids if the results page takes more than 2 minute to load. Biointerpreter will search your gene identifiers in the comprehensive annotation database. It will retrieve all the necessary annotation from the database. Then it will sort out the results in to different category like functions, disease, pathway, chromosome, etc.

The result will be categorized in to following categories.

Summary report
Chromosome
Pathway Function
Disease
Localization
Gene Expression
Cancer Gene expression
Protein domain
Protein Ligand
Tissue expression
Gene Ontology
Hot molecules
Drug response

Biointerpreter Results

Under each category, there will be subcategory / elements. For example a list of functions will be displayed under the function category. For each function, the number of genes supporting the function, and P value will be given. Biointerpreter counts the number of genes in the query list supporting each function and will find the significance. A set of significant functions will be retrieved and displayed. NOTE: Some categories are not available in the demo version.

Summary Report

Summary report gives the following details

Study Name: The study name entered by the user in the previous page.
ID type: The type of ID queried by the user.
IDs Entered: Number of ids you have pasted in the “Paste ids” textbox
Non-redundant Ids: If any id in the list is repeated, the redundancy will be removed. Only the unique list of ids will be taken to query the database.
Number of genes found: Number of genes found in the database for the IDs entered
Number of ids not found: Ids not found in the database.
The resutl views can be exported to Excel sheet and can be saved in the computer.

The user can view the list of genes found in the database by clicking “Number of Genes Found” button. It displays the genes found with symbols and gene name. Unigene in this page is linked to detailed annotation of the corresponding gene.

P value:

P value (Probability value) is the probability of getting the same result with a random set of gene identifiers. Chi-square test is used to calculate the P value. Chi-square is a common statistical method used to derive P value of the (input) observed data and expected data. If the P value is about 0.10, it means there is a 10% probability that the deviation is only due to chance and other factors are involved. P value less than 0.05 considered as significant. The results are sorted by P value in increasing order.

Viewing the Resutl Categories & Interpretation

Example - Function

To view the functions related to the queried genes in the function table. The detailed function table is listed below.

Biointerpreter finds the list of functions that are over represented in query list. The details are

Function
Number of genes involved in the functions in query list
The number in the square bracker [] specified the number of genes involved in the functions in genome.

To view the genes involved in a function

Select the function by clicking the corresponding check box
click the "Table view" button

The list of genes associated with fucntions selected will be displayed at the right window with the following information:

Query ID

Unigene ID with link to detailed annotation

Gene name

Gene Symbol

Functions

To view genes involved in all the selected functions:

Select the Functions by clicking on the corresponding check boxes.
Select ‘AND’ radio button at the bottom.
Click the ‘Table View’ button.

In the above figure, the user would like to view the genes involved in both Angiogenesis and Antigen Processing & Presentation. Biointerpreter finds the genes involved in both of the functions and reports in the result window.

Number of related keywords of the function found in the comprehensive annotation of the gene is displayed under each function. This number is hyperlinked to get detailed annotation of the gene. Related keywords for the function will be highlighted in the detailed annotation.

For example, in the above figure,

2 related keywords of “Angiogenesis” were found in Hs.109225.
2 related keywords of “Antigen processing and Presentation” were found in Hs.111779.
If you click on Angiogenesis found in Hs.109225 it will give you detailed annotation for Hs.109225