Introduction to Microarray Analysis- Stratagene ArrayAssist

Transcriptomics
Patrick Kemmeren
European Bioinformatics Institute
Genomics Lab, UMC Utrecht
What are microarrays ?
Transcriptomics?

hybridisation
RNA extract
Sample
Array design
hybridisation
labelled
nucleic acid
array
RNA extract
Sample
hybridisation
RNA extract
Sample
hybridisation
RNA extract
Sample
hybridisation
RNA extract
Sample
Experiment
genes
Samples
Genes
Gene expression matrix
Microarray data and annotation
Traditions of data sharing in Life Sciences
Data used in publications should be made available so that
the experiments can be reproduced and the conclusions can be verified
the others can build on other’s results
In genome sequencing this has evolved into submissions to public sequence databases DDBJ/EMBL/Genbank – most journals require such submissions
Sharing microarray data – which data?
MGED standards - MIAME
MIAME 6 parts of a microarray experiment
MGED – MIAME
Microarray experiment
Samples
Extracts
Labelled Extracts
Colours related to labels
Hybridizations
Shapes related to array designs
Experiment name
Rustici et al., S. pombe cell-cycle mutant data (2004)
Submissions Database
Retrieval of raw & processed data for analysis
Gene, sample, and experiment centric queries,
Submission support
Curation
MAGE-ML
XML
Visualisation
Data download
Data upload
User
Functionality
Database
Architecture
MAGE-ML
External
Application
Submission and annotation tool
Potential local data annotation tool
Based on MIAME concepts
Accepts protocol, array and experiment submissions
User accounts allow re-use of protocols and arrays
Works with your own or commercial arrays
MIAMExpress
MIAMExpress schema
Submissions Database
Retrieval of raw & processed data for analysis
Gene, sample, and experiment centric queries,
Submission support
Curation
MAGE-ML
XML
Visualisation
Data download
Data upload
User
Functionality
Database
Architecture
MAGE-ML
External
Application
ArrayExpress
http://www.ebi.ac.uk/arrayexpress

A public repository for microarray data at the EBI
Online (MIAMExpress)
Submissions
ArrayExpress data - by organism
Total ~ 7000 hybridisations
Submissions Database
Retrieval of raw & processed data for analysis
Gene, sample, and experiment centric queries,
Submission support
Curation
MAGE-ML
XML
Visualisation
Data download
Data upload
User
Functionality
Database
Architecture
MAGE-ML
External
Application
Gene-centric Query Prototype
http://www.ebi.ac.uk/aedw/ArrayExpress_main.html
Gene-centric Query Prototype
- Driven by a BioMart backend
Gene-centric Query Prototype
Submissions Database
Retrieval of raw & processed data for analysis
Gene, sample, and experiment centric queries,
Submission support
Curation
MAGE-ML
XML
Visualisation
Data download
Data upload
User
Functionality
Database
Architecture
MAGE-ML
External
Application
Expression Profiler
http://www.ebi.ac.uk/expressionprofiler

An online microarray data analysis platform
What can you do with the data?
What can you do with the data?
...view as a heatmap...
Expression Profiler
Data Viewer Component
What can you do with the data?
...cluster the data...
Expression Profiler
Hierarchical Clustering Component
What can you do with the data?
...look at GeneOntology enrichment of a selected cluster ...
Expression Profiler
GO Annotation Component
What can you do with the data?
... check out how clusterings compare ...
Expression Profiler
Clustering Comparison Component
What can you do with the data?
Expression Profiler
Threeway Similarity Analysis
... integrate several data types together ...

Data Selection
Data Transformation
Missing Value Imputation
Hierarchical Clustering & K-groups Clustering
Clustering Comparison
Signature Algorithm
Sequence Homology
SPEXS: Promoter Discovery
Visual Pattern Matching
Ordination (COA, PCA)
Between Group Analysis
Three-way Similarity Analysis
GO Annotation
Uses:
ArrayExpress suite of tools
Standalone tool
Locally installed (UJI, UMC Utrecht)
Teaching tool
Pipelines, workflows, high-throughput analysis
Available Components
Original EP Development:
Jaak Vilo (Tartu)
Patrick Kemmeren (Utrecht)
Misha Kapushesky
EP:NG Framework Development:
Patrick Kemmeren (Utrecht)
Misha Kapushesky
Caroline Johnston (UCL)
Visualization Components:
Misha Kapushesky
Steffen Durinck (Leuven)
Phil Hyoun Lee
Clustering Comparison:
Aurora Torrente
Christine Körner (Leipzig)
PCA/COA/BGA:
Aedín Culhane (Cork)
Signature Algorithm:
Jan Ihmels (Tel-Aviv)
Gene Ordering:
Karlis Freivalds (Riga)
Normalisation:
Caroline Johnston (UCL)
Web Services:
Antonio Estruch (UJI)
Acknowledgements
EBI Microarray Informatics Team

Alvis Brazma, Head of Microarray Informatics Group
Ahmet Oezcimen, Scientist (Oracle DBA)
Anastasia Samsonova, PhD student
Anjan Sharma, Scientist (Software Developer)
Anna Farne, Scientist (Curation)
Aurora Torrente, PhD Student
Bhuwan Tiwari, Trainee
Catherine Leroy, Summer Student
Ele Holloway, Scientist (Curation)
Gabriella Rustici, Scientist (Postdoc)
Gaurab Mukherjee, Scientist (Curation)
Gonzalo Garcia Lara, Scientist (Web Designer/Programmer)
Helen Parkinson, Scientist (Curation Coordinator)
Jaak Vilo, Consultant
Lev Soinov, Scientist (Postdoc Wellcome Trust)
Misha Kapushesky, Scientist (Scientific Application Programmer)
Mohammadreza Shojatalab, Scientist (Database Programmer)
Niran Abeygunawardena, Scientist (Web Designer/Programmer)
Patrick Kemmeren, Consultant
Per Lilja, Scientist (Database Programmer)
Philippe Rocca-Serra, Scientist (Nutrigenomics Proj. Coordinator)
Pierre Marguerite, Summer Student
Richard Coulson, Scientist (Biosapiens Project)
Sergio Contrino, Scientist (Database Programmer)
Steffen Durinck, Student
Susanna-Assunta Sansone, Scientist (Toxicogenomics Proj. Coordinator)
Tim Rayner, Scientist (Curation)
Ugis Sarkans, Scientist (Database Development Coordinator)