ArrayExpress
- Database of gene expression and other microarray data at the European Bioinformatics Institute (EBI), located at the Wellcome Trust Foundation in Cambridge, UK.
- http://www.ebi.ac.uk/arrayexpress

RNA GENiE
- Database to locate RNA genes based on the premise that stable, functional RNAs share common structural elements and that sequences corresponding to these elements would occur preferentially in RNA genes, from the Hoolbrook Laboratory, Lawrence Berkeley Na
- http://rnagene.lbl.gov/

MERNA
- A data base of metal binding sites of RNA, from the Holbrooke Laboratory, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
- http://merna.lbl.gov/

SymAtlas
- Database on gene function and structure, from the Genomics Institute of the Novartis Research Foundation.
- http://symatlas.gnf.org

IRES Database
- Database on gene expression with information on Internal Ribosome Entry Sites IRES. From INSERM, the French Institute of Health.
- http://ifr31w3.toulouse.inserm.fr/iresdatabase

RNase P Database
- A compilation of RNase P sequences, sequence alignments, secondary structures, three-dimensional structures, and accessory information.
- http://www.mbio.ncsu.edu/RNaseP/

Allen Brain Atlas
- Database of gene expression patterns in the mouse brain.
- http://www.brain-map.org

GenePaint
- Database of gene expression patterns in the mouse embryo. From Max-Planck-Institute for Biophysical Chemistry, Dept. Genes and Behavior, Göttingen, Germany
- http://www.genepaint.org

Kyoto Encyclopedia of Genes and Genomes (KEGG)
- Graphical and hypertext-based information on biochemical pathways, including metabolic and regulatory pathways cell cycle and growth factor signaling. From Kanehisa Laboratories in the Bioinformatics Center of Kyoto University, Japan.
- http://www.genome.ad.jp/kegg/

The Database of Rice Transcription Factors (DRTF)
- Free of charge database of transcription factors of rice. From CBI, Peking University, China.
- http://drtf.cbi.pku.edu.cn

Ribosomal Database Project
- From Center for Microbial Ecology, Michigan State University, USA
- http://rdp.cme.msu.edu/

GeneSifter Data Center
- Database for the GeneSifter microarray data analysis system in selected conditions. From ViZxlabs, Seattle, USA.
- http://www.genesifter.net/web/dataCenter.html

Novartis Gene Expression Atlas
- Database on gene expression in men and mice.
- http://expression.gnf.org

Rice Transcription Factor Database
- RiceTFDB is a public database of rice genes involved in transcriptional control. From the University of Potsdam, Berlin, Germany.
- http://ricetfdb.bio.uni-potsdam.de/

Gene Expression Omnibus
- Database of gene expression data from NCBI (National Center for Biotechnical Information). Includes a definable search by different characteristics.
- http://www.ncbi.nlm.nih.gov/geo/

Gene Expression in Tooth
- Database on the expression of different genes in the developing tooth.
- http://bite-it.helsinki.fi/

WormBase
- Data bases on the genetics of C elegans and related nematodes.
- http://www.wormbase.org/

Stanford Microarray Database
- Data from microarray experiments, and the corresponding image files. From Stanford University, USA.
- http://genome-www5.stanford.edu/

Exploring the Metabolic and Generic Control of Gene Expression
- Database with the data for the experiments in the paper - DeRisi et. al. Science 278: 680-686. Includes text files that can be downloaded. The original paper requires a subscription fee.
- http://cmgm.stanford.edu/pbrown/explore/

GeneExpress
- Designed for analysis of genomic regulatory sequences of higher eukaryotes. Includes several databases and programs for visualization of the information contained. From the Laboratory of Theoretical Genetics of the Institute of Cytology and Genetics of Si
- http://wwwmgs.bionet.nsc.ru/mgs/systems/geneexpress/

Mirage
- Information methodologies, tools, and technologies relating to the study of gene expression and signal transduction. From the Institute for Transcriptional Informatics (IFTI), USA.
- http://www.ifti.org/