Overview of ExonMiner

INDEX

Sample Data

Affymetrix Inc. provides demo data of GeneChip Human Gene 1.0 ST Array. You can download the data from Affymetrix web site (registration is required).

Yoshida et al. (2007) analyzed colon cancer exon array data provided above web site by using ExonMiner. You can see this analysis here.

Guide to ExonMiner

This is a flowchart of ExonMiner.

flowchart

In this web page, we explain how to use ExonMiner according to this flow chart.

1. Create your account

Your account will be created by filling this page and then an e-mail will be sent to you.

The e-mail contains the following information:

  1. Username
  2. Login Password
  3. Confirmation URL.

Please note that until you follow the confirmation URL, your account won't be activated.

2. Upload your data via FTP

For the upload of your data, you need to transfer the data via FTP. The details of the instraction are explained here.

3. Go to your personal web page

After your account is activated, you can login to your personal page. From the personal page, you can analyze your data.

4. Set the analysis options

You can set the analysis options in two-way ANOVA. The explanation of each option is shown here. All options must be specified.

5. Start the analysis

After setting all options, you can start the analysis. When the analysis of your data is completed, an announce e-mail will be sent to you.

Note that you can see the exon expression profiles of transcripts that you are interested in by the next visualization tools, even if the analysis doesn't be finished.

6. View the results

The results of analysis are compiled in Excel files. An example of an Excel file is shown here.

We developed two types of image generator and can make heatmap and barplot images optimized for exon array data. The details of the visualization tolls are here.

7. You can re-analyze with different option set over again and again

You can repeat analysis by using different option values. Also, you can upload new datasets and analyze them by ExonMiner repeatedly.