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Microrray Data Standardisation. Microarray Gene Expression Database group -- MGED December, 2000. Public data repositories for microarray data.

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Microrray data standardisation

Microrray Data Standardisation

Microarray Gene Expression Database group -- MGED

December, 2000

Public data repositories for microarray data
Public data repositories for microarray data

There is a growing consensus in the life science community for a need for public repositories of gene expression data analogous to DDBJ/EMBL/GenBank for sequences

Some of the reasons
Some of the reasons:

  • Gradually building up gene expression profiles for various organisms, tissues, cell types, developmental stages, various states, under influence of various compounds

  • Through links to other genomics databases builds up systematic knowledge about gene functions and networks

  • Comparison of profiles, access and analysis of data by third parties

  • Cross validation of results and platforms - quality control

Systematic gene expression profiling initiatives in public domain
Systematic gene expression profiling initiatives in public domain

The International Life Science Institute (ILSI) is coordinating a program undertaken by ~25 pharmaceutical and food companies to generate toxicity related gene expression data under defined experimental conditions

  • evaluate gene expression profiles in standardised test systems following exposure to toxicants

  • relate changes in gene expression to other measures of toxicity

Microarray data handling and analysis a major bottleneck calculations by jerry lanfear
Microarray data handling and analysis - a major bottleneck (Calculations by Jerry Lanfear)

  • Experiments:

    • 100 000 genes in human

    • 320 cell types

    • 2000 compounds

    • 3 time points

    • 2 concentrations

    • 2 replicates

  • Data

    • 8 x 1011 data-points

    • 1 x 1015 = 1 petaB of data

Expression data repository projects
Expression data repository projects (Calculations by Jerry Lanfear)

  • Public repositories in making:

    • GEO - NCBI

    • GeneX - NCGR

    • ArrayExpress - EBI

  • In-house databases - Stanford, MIT, University of Pennsylvania,

  • Organism specific databases: Mouse in Jackson

  • Proprietary databases - Gene Logic, NCI

Difficulties (Calculations by Jerry Lanfear)

  • Raw data are images

  • What is needed for higher level analysis and mining is gene expression matrix (genes/samples/gene expression levels)

    • lack of standard measurement units for gene expression

    • lack of standards for sample annoation

Raw data images
Raw data - images (Calculations by Jerry Lanfear)

Treated sample labeled red (Cy5)

Control data labeled green (Cy3)

Competitive hybridization onto chip

Red dot - gene overexpressed in treated sample

Green dot - gene underexpressed in treated sample

Yellow - equally expressed

Intensity - “absolute” level

red/green - ratio of expression

2 - 2x overexpressed

0.5 - 2x underexpressed

log2( red/green ) - “log ratio”

1 2x overexpressed

-1 2x underexpressed

cDNA plotted microarray

Stanford university (Yeast,1997)

Gene expression matrix
Gene expression matrix (Calculations by Jerry Lanfear)



Gene expression levels

Gene expression levels
Gene expression levels (Calculations by Jerry Lanfear)

  • What we would like to have

    • gene expression levels expressed in some standard units (e.g. molecules per cell)

    • reliability measure associated with each value (e.g. standard deviation)

  • What we do have

    • each experiment using different units

    • no reliability information

Comparing expression data

cm (Calculations by Jerry Lanfear)


Comparing expression data

Comparing expression data1

? (Calculations by Jerry Lanfear)


Comparing expression data

Comparing expression data2
Comparing expression data (Calculations by Jerry Lanfear)

Measurement units
Measurement units (Calculations by Jerry Lanfear)

  • In perspective:

    • standard controls for experiments (on chips and in the samples)

    • replicate measurements

  • Temporary solution:

    • storing intermediate analysis results (including the images) and annotations of how they were obtained - i.e., the evidence

Comparing expression data problem 2
Comparing expression data - problem 2 (Calculations by Jerry Lanfear)

  • How gene names relate in different data matrices?

  • How samples relate in different data matrices?

Sample annotation
Sample annotation (Calculations by Jerry Lanfear)

  • Gene expression data have any meaning only in the context of what are the experimental conditions of the target system

  • Controlled vocabularies and ontologies (species, cell types, compound nomenclature, treatments, etc) are needed for unambiguous sample annotation

  • Sample annotations in current public databases are typically useless

In perspective
In perspective (Calculations by Jerry Lanfear)

  • Standard units for gene expression measurements

  • Standards for sample annotation.

More immediate actions
More immediate actions (Calculations by Jerry Lanfear)

  • To understand what information about microarray experiments should be captured to make the descriptions reasonably self-contained

  • Develop data exchange format able to capture this minimum information

  • Develop recommendations how data should be normalised and what controls should be used

Mged group
MGED group (Calculations by Jerry Lanfear)

The MGED group is an open discussion group initially established at the Microarray Gene Expression Database meeting MGED 1 (14-15 November, 1999, Cambridge, UK). The goal of the group is to facilitate the adoption of standards for DNA-array experiment annotation and data representation, as well as the introduction of standard experimental controls and data normalisation methods. The underlying goal is to facilitate the establishing of gene expression data repositories, comparability of gene expression data from different sources and interoperability of different gene expression databases and data analysis software. Since 1999 the group has had two general meetings and the third one is planned for 2001

For more see www.mged.org

Mged participants including

Affymetrix (Calculations by Jerry Lanfear)





Gene Logic


Max Plank Institute




Sanger Centre


Uni Pennsylvania

Uni Washington

Whitehead Institute

MGED participants including

Working groups
Working groups (Calculations by Jerry Lanfear)

  • Microarray experiment annotations and minimum information standards (A. Brazma)

  • XML-data communication standards and interfaces (P. Spellman)

  • Ontology for sample description (M. Bittner)

  • Cross platform comparison and normalisation (F.Holstege, R.Bumgarner)

  • Future user group - queries, query languages and data mining (M. Vingron)

Mged state of art
MGED state of art (Calculations by Jerry Lanfear)

  • Formulation of the “minimum information about a microarray experiment” (MIAME) to ensure its interpretability and reproducibility

  • Data exchange format based on XML - microarray markup language (MAML) submitted to OMG in November

Miame six parts
MIAME six parts: (Calculations by Jerry Lanfear)

1. Experimental design: the set of the hybridisation experiments as a whole

2. Array design: each array used and each element (spot) on the array

3. Samples: samples used, the extract preparation and labeling

4. Hybridizations: procedures and parameters

5. Measurements: images, quantitation, specifications

6. Controls: types, values, specifications

see www.mged.org for details

Miame concepts
MIAME concepts (Calculations by Jerry Lanfear)

  • MIAME is aimed at co-operative data submitter

  • Concept of “qualifier, value, source” lists, where source is either user defined or an external reference

  • Reusable information can be referenced, but should be provided at least once (array descriptions, standard protocols)

  • Raw data should be reported, together with the authors interpretations

Microrray data standardisation
MAML (Calculations by Jerry Lanfear)

  • MAML is an XML based data exchange format able to capture MIAME compliant information

  • The work is still in progress, the first draft has been submitted to OMG as a data exchange standard for microarray data

Maml concepts
MAML concepts (Calculations by Jerry Lanfear)

  • Annotations + data; data can be given as a set of external 2D matrices

  • Data format independent on particular scanner or image analysis sofwater

  • Sample and treatment can be represented as a DAG

  • Concept of composite images and composite spots

Sample and treatment representation
Sample and treatment representation (Calculations by Jerry Lanfear)

Sample 1

Sample 2

Sample 3


Array 2

Array 1

Expression matrix raw and processed

Images (Calculations by Jerry Lanfear)




Gene expression levels

Spot/Image quantiations

Expression matrix - raw and processed

Microarray image analysis data representation
Microarray image analysis data representation (Calculations by Jerry Lanfear)








composite images

e.g., green/red ratios

primary images

Maml future
MAML future (Calculations by Jerry Lanfear)

  • The NOMAD microarray LIMS system will export data in MAML format

  • ArrayExpress and GEO will import data in MAML format

  • We hope that OMG will accept MAML as the industry standard

  • We hope that MAML will become a defacto standard

Mged steering committee
MGED steering committee (Calculations by Jerry Lanfear)

  • Meeting in Bethesda on 17 Nov 2000

  • MIAME accepted and a publication urging the journals and funding agencies to adopt it will be prepared

  • MGED will become ISCB Special Interest Group

  • Next general MGED meeting in Stanford, March 29-31