Links

Microarray Standardization and Data Quality Control

Functional Genomics, Bioinformatics and Systems Biology projects

Public Microarray Gene Expression Repositories and Databases

Microarray Technology Resource

European Microarray Facilities

 

At this page we present links to the microarray community in Europe with special attention to projects related to standards and standardization of microarray technology and data analysis. We also want to link to Systems Biology related projects and to microarray core facilities in Europe.

If you find any errors or want your link added to this page, please send an email to

 

Microarray Standardization and Data Quality Control

  • EMERALD Empowering the Microarray-Based European Research Area to Take a Lead in Development and Exploitation is a project to establish and disseminate quality metrics (QC), microarray standards and best laboratory practices (QA) throughout the European microarray community.
  • MGED The Microarray and Gene Expression Data (MGED) Society is an international organization of biologists, computer scientists, and data analysts that aims to facilitate the sharing of data generated using the microarray and other functional genomics technologies for a variety of applications including expression profiling.
  • MIAME describes the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.
  • NIST The National Institute of Standards and Technology is a federal technology agency that develops and promotes measurement, standards, and technology.
  • ERCC The External RNA Controls Consortium (ERCC) is composed of representatives from the public, private, and academic sectors, working together to produce external RNA spike-in controls that will be useful for sample control on a variety of microarray platforms and by RT-PCR. These platform-independent control materials are needed for performance evaluation of reproducibility, sensitivity, and robustness in gene expression analysis.
  • MAQC The purpose of the MicroArray Quality Control (MAQC) project is to provide quality control tools to the microarray community in order to avoid procedural failures and to develop guidelines for microarray data analysis by providing the public with large reference datasets along with readily accessible reference RNA samples.- Download data from ArrayExpress.
  • MIACA The MIACA initiative on Minimum Information About a Cellular Assay develops guidelines for the description of experiments and data from cell based assays.

 

Functional Genomics, Bioinformatics and Systems Biology projects

  • MOLTOOLS Advanced Molecular Tools for Array-based Analyses of Genomes. New molecular tools will give us the opportunity to identify all molecules encoded in our genomes, even at the single-molecule level, and to do this in individual patient samples. The EU FP6 project MolTools aims to promote the development and implementations of such tools by bringing together leading European groups in the area of molecular technology development.
  • ESF Programme on Frontiers of Functional Genomics. This European Science Foundation progam will connect the most promising developments in functional genomics technologies with the expanding concept of systems biology, focusing particularly on applications in biomedicine, as well as the environment and implications for society at large.
  • Bioconductor is an open source and open development software project for the analysis and comprehension of microarray and genomic data.
  • DIAMONDS Dedicated Integration And Modelling Of Novel Data and prior knowledge to enable Systems biology. The DIAMONDS project aims to demonstrate the power of a Systems Biology approach to study the regulatory network structure of the most fundamental biological process in eukaryotes: the cell cycle. An integrative approach will be applied to build a basic model of the cell cycle, in four different species including S. cerevisiae (budding yeast), S. pombe (fission yeast), A. thaliana (weed, model plant) and human cells.
  • EMBRACE A European Model for Bioinformatics Research and Community Education. The objective of EMBRACE is to draw together a wide group of experts throughout Europe who are involved in the use of information technology in the biomolecular sciences. The EMBRACE Network of Excellence will optimise informatics and information exploitation by pure and applied biological scientists in both the academic and commercial sectors.
  • BioSapiens A European Virtual Institute for Genome Annotation. The objective of the BioSapiens is to provide a large scale, concerted effort to annotate genome data by laboratories distributed around Europe, using both informatics tools and input from experimentalists.
  • ELIXIR European Life Sciences Infrastructure For Biological Information. The mission of ELIXIR is to construct and operate a sustainable infrastructure for biological information in Europe to support life science research and its translation to medicine and the environment, the bio-industries and society.

 

Public Microarray Gene Expression Repositories and Databases

  • ArrayExpress is a public repository for microarray data, which is aimed at storing MIAME-compliant data in accordance with MGED recommendations. The ArrayExpress Data Warehouse stores gene-indexed expression profiles from a curated subset of experiments in the repository.
  • GEO Gene Expression Omnibus is a gene expression/molecular abundance repository supporting MIAME compliant data submissions, and a curated, online resource for gene expression data browsing, query and retrieval.
  • SMD Stanford Microarray Databse is a research tool and archive that allows hundreds of researchers worldwide to store, annotate, analyze and share data generated by microarray technology. SMD supports most major microarray platforms, and is MIAME-supportive and can export or import MAGE-ML.
  • Arex The Arabidopsis Gene Expression Database. Arex stores genome-wide (Affymetrix microarray) and gene-specific (in situ, GFP-reporter, etc.) Arabidopsis spatial gene expression data.
  • TAIR The Arabidopsis Information Resource maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.
  • MGI Mouse Genome Informatics provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse.
  • RGD The Rat Genome Database curates and integrates rat genetic and genomic data and provides access to this data to support research using the rat as a genetic model for the study of human disease.
  • GO The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
  • Reactome a curated knowledgebase of biological pathways. The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.
  • KEGG Kyoto Encyclopedia of Genes and Genomes. A grand challenge in the post-genomic era is a complete computer representation of the cell, the organism, and the biosphere, which will enable computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information. Towards this end we have been developing a bioinformatics resource named KEGG as part of the research projects of the Kanehisa Laboratories in the Bioinformatics Center of Kyoto University and the Human Genome Center of the University of Tokyo.

 

Microarray Technology Resources

  • BioChipNet, The BioChipNet database is a comprehensive and searchable information platform on microarrays and related fields such as microfluidics and bioinformatics.
  • Genome Chip, Basic information on DNA microarray technology and a list of academic and industrial links.
  • Biocompare, Microarrays, The Buyers Guide for Life Scientists.

 

European Micraorray Facileties

Belgium:

Czech Republic:

  • Microarray Core Facility, Institute of Molecular Genetics, Academy of Science of the Czech Republic (ASCR), Czech Republic

Finland:

France:

Germany:

Hungary:

The Netherlands:

Norway:

Sweeden:

Switzerland:

UK: