Microarray Databases and MIAME (Minimum Information About a Microarray Experiment)

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Microarray Databases and MIAME (Minimum
Information About a Microarray Experiment)

• Yong Liu
• Bioinformatics Unit

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Outline

• Review of microarray technology from
  data/database perspective
• Motivation behind the MIAME standard
• MIAME whats in it?
• Current existing microarray databases
• Future development

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DNA Microarray Technology
Cy3 550 nm
Cy5 650 nm
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Context is Everything !

• An observed phenotype is specific for the
  conditions under study (Pat Brown, Stanford
  University)
• Information recorded in microarray database
  should be used on standalone basis
• Any background information
• Automated data analysis and mining, i.e. not only
  on record-by-record basis
• Data from different laboratories and different
  technology platforms

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Capturing Data and Meta-data in Microarray
Experiments
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How Much Data?

• Experiments
• 100 000 genes in human
• 320 cell types
• 2000 compounds
• 3 time points
• 2 concentrations
• 2 replicates
• Data volume
• 8 x 1011 data-points
• 1 x 1015 1 petaB of data

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Gene Expression Matrix
The final gene expression matrix (on the right)
is needed for higher level analysis and mining.
?
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MGED and MIAME

• A need to establish a public repository or
  repositories for microarray gene expression data
  became apparent in 1998, which requires data
  standards
• MGED-1 (Microarray Gene Expression Database)
  Group November 14-15, 1999, Cambridge, UK
• Established five working groups, including the
  microarray data annotation group (MIAME)
• MGED-2 May 25 - 27, 2000, Heidelberg, Germany
• Endorsed a MIAME draft
• MGED-3 March 29-31, 2001, Stanford University
• Adopted MIAME 1.0
• MGED-4 Feb. 13-16, 2002, Boston
• Adopted MIAME 1.1

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MIAME Six Parts
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MIAME Part 1 - Experimental Design the set of
the hybridisation experiments as a whole

• Author, contact information, citations
• Type of experiment (e.g., time course, normal vs
  diseased comparison)
• Experimental factors i.e. tested parameters in
  the experiment (e.g. time, dose, genetic
  variation, response to a compound)
• List of organisms used in the experiment
• List of platforms used

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MIAME Part 2 - Array Design each array used and
each element (spot) on the array

• Array design related information (e.g. platform
  type insitu synthesized or spotted, array
  provider, surface type glass, membrane, other,
  etc)
• Properties of each type of elements on the array,
  that are generated by similar protocols (e.g.
  synthesized oligos, PCR products, plasmids,
  colonies, others) may be simple or composite
  (Affymetrix)
• Each element (spot) on the array

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MIAME Part 3 - Samples samples used, the extract
preparation and labeling

• Sample source and treatment
• Hybridisation extract preparation
• Laboratory protocol, including extraction method,
  whether RNA, mRNA, or genomic DNA is extracted,
  amplification method
• Labelling
• Laboratory protocol, including amount of nucleic
  acids labelled, label used (e.g. Cy3, Cy5, 33P,
  etc)

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MIAME Part 4 - Hybridizations procedures and
parameters

• The solution (e.g. concentration of solutes)
• Blocking agent
• Wash procedure
• Quantity of labelled target used
• Time, concentration, volume, temperature
• Description of the hybridisation instruments

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MIAME Part 5 - Measurements images,
quantitation, specifications

• Scanning information
• Scan parameters, including laser power, spatial
  resolution, pixel space, PMT voltage
• Laboratory protocol for scanning, including
  scanning hardware and software used
• Image analysis information
• Image analysis software specification
• All parameters
• Summarised information from possible replicates

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MIAME Part 6 Normalization types, values,
specifications

• Normalisation strategy (spiking, housekeeping
  genes, total array, other)
• Normalisation algorithm
• Control array elements

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Current Existing Microarray Databases

• Local Installation
• AMAD, GeneDirector, mAdb, maxdSQL, NOMAD
• Public Queries only
• ChipDB, RAD
• Public Queries and Local Installation
• SMD
• Public Data Deposition and Queries
• ArrayExpress, GEO, GXD
• GeneX and GeNet

FOR MORE INFO...
Margaret Gardiner-Garden and Timothy G.
Littlejohn, A comparison of micoarray databases,
Briefings in Bioinformatics, May 2001
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MIAME-compliant Systems

• Different labs have different needs lab-centric
  system is more desirable
• MIAME-compliant microarray database systems are
  still under development
• Commerical
• GeneTraffic (www.iobion.com)
• PARTISAN arrayLIMS (www.clondiag.com)
• Rosetta Resolver (www.rosettabio.com)
• .
• OpenSource
• GeneX and NOMAD, among others, are still under
  development to be MIAME-compliant,

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Future Development

• Establishing MIAME-compliant databases
• Different labs continue to develop their own
  systems
• Data exchange format (MAGE-ML) allowing to
  communicate MIAME information
• Microarray data has no central DB yet
  distributed data queries and data mining?
• HTTP/XML
• SOAP (Simple Object Access Protocol)
• WDSL(Web Services Description Language)
• UDDI (Universal Description, Discovery, and
  Integration)