Review of Array Express

Thomas, M.D.

Georgia Institute of Technology

21 June, 2006

What is a Microarray Database?

• Collection of microarray data published or unpublished.

• Includes cel files, samples, raw data, author, paper title, platform.

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

What do we use it for?

• Create PADRE images

• Compare complexities between more/less complex organisms

• Over all goal: Invalidate results

What is Array Express?

• Public repository for microarray data

• Objective: Store-house for data, platforms

• Has been used especially for yeast data collection

Array Express For Dummies• Select what organism

you want to search on the left.

• Yeast is the queried term in this aspect.

Viewing Search Results

• Use chip platform selection tab to get desirable platform.

• After your search several results will pop up.

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.

Gathering Data

• Click on AE link, then click on retrieve data.

• Cel files are at the bottom of the page.

Further Supplemental Data• Further data found

on initial search page

• Author, article, publication information

MAGE ML

• Microarray Gene Expression- Markup Language

• Based on XML

• Describes Microarray data and history

• User- friendly tools providing web form interface

MAGE ML in Array Express

• After AE link

• Used to organize data

What it Looks Like

Draw Backs

• No quality control information

• Database is limited

• Not efficient: time consuming trial and error

• Can’t find published papers

• No accession numbers

• No probe locations

Positive Features

• Sample size view

• Cel files

• Diverse database (Platforms, Organisms)

• Publication Info.

• Author, article info

• Supplemental data

Thank You

• Georgia Tech

• Dr. Wang

• The Stokster

• Ricky

• Malcolm Thomas