BioIntepreter Help File

CompanyName

Biointerpreter User Manual

NOTE: Graphical presentation is disabled and 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

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.

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.

To View the gene details in tablular format:

Each category will display the members of the category, number of genes supporting the member and P value for the member. In the first result page the following operations can be performed

View the pie chart for the selected functions / disease / localization etc.
View the details for the selected subcategory / elements in the table view with AND / OR query.

(Here we have explained for functions. The same can be implied all the result categories)

AND / OR query for the table view

AND query – The genes which are associated with all the selected functions will be displayed.

OR query- The genes which are associated with any one of the selected functions will be displayed in the table view.