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 Collection of microarray data published or unpublished.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