Review of Array Express Thomas M D Georgia

What is a Microarray Database? • Collection of microarray data published or unpublished. •

Ideal Database • Simple: “Ignorant Usage” • Clearly presented features i. e. cel files,

What do we use it for? • Create PADRE images • Compare complexities between

What is Array Express? • Public repository for microarray data • Objective: Store-house for

Array Express For Dummies • Select what organism you want to search on the

Viewing Search Results • Use chip platform selection tab to get desirable platform. •

Process of Selection • Select a data set. • Bunch of samples. • Chip

Gathering Data • Click on AE link, then click on retrieve data. • Cel

Further Supplemental Data • Further data found on initial search page • Author, article,

MAGE ML • Microarray Gene Expression- Markup Language • Based on XML • Describes

MAGE ML in Array Express • After AE link • Used to organize data

Draw Backs • • • No quality control information Database is limited Not efficient:

Positive Features • • • Sample size view Cel files Diverse database (Platforms, Organisms)

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

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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 • Collection of microarray data published or unpublished.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