Review of Array Express

1
Review of Array Express

• Thomas, M.D.
• Georgia Institute of Technology
• 21 June, 2006

2
What is a Microarray Database?

• Collection of microarray data published or
  unpublished.
• Includes cel files, samples, raw data, author,
  paper title, platform.

3
Ideal Database

• Simple Ignorant Usage
• Clearly presented features i.e. cel files,
  normalization, Q.C.
• Large pool of organisms and platforms
• Links to paper, author, and institution,
  citations
• Probe locations

4
What do we use it for?

• Create PADRE images
• Compare complexities between more/less complex
  organisms
• Over all goal Invalidate results

5
What is Array Express?

• Public repository for microarray data
• Objective Store-house for data, platforms
• Has been used especially for yeast data collection

6
Array Express For Dummies

• Select what organism you want to search on the
  left.
• Yeast is the queried term in this aspect.

7
Viewing Search Results

• Use chip platform selection tab to get desirable
  platform.
• After your search several results will pop up.

8
Process of Selection

• Select a data set.
• Bunch of samples.
• Chip and AE link figures to get cel files.
• All information is listed below your selection.

9
Gathering Data

• Click on AE link, then click on retrieve data.
• Cel files are at the bottom of the page.

10
Further Supplemental Data

• Further data found on initial search page
• Author, article, publication information

11
MAGE ML

• Microarray Gene Expression- Markup Language
• Based on XML
• Describes Microarray data and history
• User- friendly tools providing web form interface

12
MAGE ML in Array Express

• After AE link
• Used to organize data

13
What it Looks Like
14
Draw Backs

• No quality control information
• Database is limited
• Not efficient time consuming trial and error
• Cant find published papers
• No accession numbers
• No probe locations

15
Positive Features

• Sample size view
• Cel files
• Diverse database (Platforms, Organisms)
• Publication Info.
• Author, article info
• Supplemental data

16
Thank You

• Georgia Tech
• Dr. Wang
• The Stokster
• Ricky
• Malcolm Thomas