Introduction to Microarray Analysis- Stratagene ArrayAssist

RNA extractSample Experiment Gene expression data matrix normalization... Sample annotationGene annotation Gene expression matrix Microarray data and annotation... MIAMExpress DatabaseS

Patrick Kemmeren European Bioinformatics Institute Genomics Lab, UMC Utrecht

mRNA cDNA

hybridise to microarray

What are microarrays ?

Transcriptomics?

RNA extract

Sample

Experiment

Gene expression data matrix normalization

Sample annotation

Gene

annotation

Gene expression matrix

Microarray data and annotation

Traditions of data sharing in Life

• 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

Array Sample

• Sample source

• Sample treatments

• Extraction protocol

• Labeling protocol

• Array design information

• Location of each element

• Description of each element Hybridization protocol

MIAMExpress Database

Submissions Database

Retrieval of raw &

processed data for analysis

Gene, sample, and experiment centric queries,

Submission

ML

MAGE-XML

Visualisation Data download

Data upload

User Functionality

Database Architecture

ML

MAGE-External Application

ArrayExpress Repository

AE Data Warehouse

• 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

Create Account

Sample1 SamplenExtracts 1…n Extracts 1…n

Submit

Array1 ArraynData1 DatanLabels 1…n Labels 1…n

Curation ArrayExpress

MAGE-ML export using MAGEstk API

Hyb protocol Sample protocol

MIAMExpress schema

MIAMExpress Database

Submissions Database

Retrieval of raw &

processed data for analysis

Gene, sample, and experiment centric queries,

Submission

ML

MAGE-XML

Visualisation Data download

Data upload

User Functionality

Database Architecture

ML

MAGE-External Application

ArrayExpress Repository

AE Data Warehouse

http://www.ebi.ac.uk/arrayexpress

• A public repository for

microarray data at the EBI

Submissions by pipelines

MEXP SMDB CAGE TIGR NASC UMCU SNGR RZPD FLYC AFMX EMBL MANP RUBN DKFZ WMIT HGMP

Online (MIAMExpress) Submissions

ArrayExpress data - by organism

Homo sapiens 23%

Homo sapiens Mus musculus Arabidopsis thaliana

Schizosaccharomyces pombe

OtherDrosophila melanogaster Saccharomyces cerevisiae Rattus norvegicus

Caenorhabditis elegans Apis mellifera

Danio rerio Gerbera hybrid cultivar Hordeum vulgare Medicago truncatula Pan troglodytes Platichthys flesus Pseudomonas aeruginosa

MIAMExpress Database

Submissions Database

Retrieval of raw &

processed data for analysis

Gene, sample, and experiment centric queries,

Submission

ML

MAGE-XML

Visualisation Data download

Data upload

User Functionality

Database Architecture

ML

MAGE-External Application

ArrayExpress Repository

AE Data Warehouse

Gene-centric Query Prototype

Gene-centric Query Prototype

New!

- Driven by a BioMart backend

Gene-centric Query Prototype

New!

MIAMExpress Database

Submissions Database

Retrieval of raw &

processed data for analysis

Gene, sample, and experiment centric queries,

Submission

ML

MAGE-XML

Visualisation Data download

Data upload

User Functionality

Database Architecture

ML

MAGE-External Application

ArrayExpress Repository

AE Data Warehouse

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?

cluster

the data Hierarchical Clustering Component Expression Profiler

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

Original EP Development:

EP:NG Framework Development:

Visualization Components:

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)