Norwegian University of Science and Technology (NTNU)
Department of Clinical and Molecular Medicine
Functional Genomics (FUGE) at the Research Council of Norway

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 FGED 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.

• 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 behaviours from genomic and molecular information. Towards this end a bioinformatics resource named KEGG has been developed 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 Standardization and Data Quality Control

• FGED The Functional Genomics Data Society (FGED) Society is an international organization of biologists, computer scientists, and data analysts that aims to facilitate the sharing of data generated using 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 and high througput sequencing platforms.  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.