proteomics and Analysis of Gene expression
ArrayExpress (European Bioinformatics Institute)
http://www.ebi.ac.uk/arrayexpress/
ArrayExpress is a public repository for MGED (http://www.mged.org/)
compliant annotated microarray (gene expression) data. Each microarray project
in the database includes two main components: the Array (information about
the array itself) and the Experiment (information about experimental factors
and the actual experimental data). Information about protocols is also included.
DRAGON Database (Kennedy Krieger Institute and Johns Hopkins)
http://pevsnerlab.kennedykrieger.org/dragon.htm
DRAGON (Database Referencing of Array Genes Online) is a database of integrated
protein information with data drawn from many other public databases, such
as Unigene, SWISS-PROT, Pfam, and KEGG). Thus, searching DRAGON can provide
information about many of the biological characteristics of the genes in
a microarray data set to enhance the analysis of microarray data. DRAGON
can also be used to annotate data, and has other tools for data visualization.
GEO (Gene Expression Omnibus, NCBI)
http://www.ncbi.nlm.nih.gov/geo/
GEO is a public repository for a variety of high-throughput experimental
data including data from microarray-based experiments measuring mRNA, genomic
DNA, and protein abundance. Other types of data include non-array techniques
such as serial analysis of gene expression (SAGE), and mass spectrometry
proteomic data. GEO contains approximately a billion individual gene expression
measurements, from over 100 organisms and a wide range of biological issues.
Data is also grouped into GEO DataSets (GDS). GDS are curated sets of GEO
Sample data. Each record represents a collection of biologically and statistically
comparable GEO.
Human Protein Atlas (HPI)
http://www.proteinatlas.org/
HPI illustrates the expression and localization of proteins in a variety
of normal human tissues and cancer cells. Data is displayed as high resolution
images of immunohistochemically stained tissue sections. Proteins (genes)
can be found by specific searches (gene/protein name/id or classification,
such as kinase or protease) or by browsing chromosomes.
Integr8 (European Bioinformatics Institute)
http://www.ebi.ac.uk/integr8/EBI-Integr8-HomePage.do
Integr8
provides access to integrated information about completed genomes and proteomes.
It provides access to a wide variety of information drawn from many sources.
Types of data include species descriptions, sequence and descriptive data, literature,
statistical analyses of genomes and proteomes. Some of the data sources include
EMBL, UniProt, CluSTr and GO.
SAGE Genie
http://cgap.nci.nih.gov/SAGE
The
SAGE Genie website provides visual displays of human and mouse gene expression,
based on a an analytical process that reliably matches SAGE tags to known genes.
Recently, a reference database of SNP-associated alternative tags has been incorporated
into SAGE Genie
SageNet
http://www.sagenet.org/
A web resource providing access to several collections of SAGE Data as well
as to SAGE Tag to Gene Maps, protocols, software, and literature covering
methods, reviews, and many types of experimental analyses using SAGE.
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