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Microarray Databases

Microarray databases store microarray gene expression data and make it available for analysis. There are two types - public repositories that adhere to standards and are designed for broad use, and specialized repositories associated with a particular entity that may have restrictions on access or use. Some major public databases include Gene Expression Omnibus, ArrayExpress, and Genevestigator.

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Microarray Databases

Microarray databases store microarray gene expression data and make it available for analysis. There are two types - public repositories that adhere to standards and are designed for broad use, and specialized repositories associated with a particular entity that may have restrictions on access or use. Some major public databases include Gene Expression Omnibus, ArrayExpress, and Genevestigator.

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william919
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© © All Rights Reserved
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Microarray databases

A microarray database is a repository containing microarray gene expression data. The key uses of a
microarray database are to store the measurement data, manage a searchable index, and make the data
available to other applications for analysis and interpretation (either directly, or via user downloads).

Microarray databases can fall into two distinct classes:

1. A peer reviewed, public repository that adheres to academic or industry standards and is
designed to be used by many analysis applications and groups. A good example of this is
the Gene Expression Omnibus (GEO) from NCBI or ArrayExpress from EBI.
2. A specialized repository associated primarily with the brand of a particular entity (lab,
company, university, consortium, group), an application suite, a topic, or an analysis method,
whether it is commercial, non-profit, or academic. These databases might have one or more
of the following characteristics:
A subscription or license may be needed to gain full access,
The content may come primarily from a specific group (e.g. SMD, or UPSC-BASE), the
Immunological Genome Project
There may be constraints on who can use the data or for what purpose data can be
used,
Special permission may be required to submit new data, or there may be no obvious
process at all,
Only certain applications may be equipped to use the data, often also associated with
the same entity (for example, caArray at NCI is specialized for the caBIG),
Further processing or reformatting of the data may be required for standard applications
or analysis,
They claim to address the 'urgent need' to have a standard, centralized repository for
microarray data. (See YMD, last updated in 2003, for example),
There is a claim to an incremental improvement over one of the public repositories,
A meta-analysis application, which incorporates studies from one or more public
databases (e.g. Gemma primarily uses GEO studies; NextBio uses various sources)

Some of the most known public, curated microarray databases are:


Microarray
Sample
Database Scope experiment As of date
profiles
sets

ArrayTrack hosts both public and private


ArrayTrack data, including MAQC benchmark data, 1622 50,093 Feb 2012
with integrated analysis tools

Hosts NCI data with integrated analysis


NCI mAdb ? 105,000 Mar 2012
and statistics tools
Open access across all immune system
ImmGen database cells; expression data, differential 267 1059 Jan 2012
expression, coregulated clusters, regulation

Gene expression search engine based on


manually curated, well annotated public October
Genevestigator 3228 232,855
and proprietary microarray and RNA-seq 2016
datasets

Gene Expression any curated MIAME compliant molecular October 28,


25859 641770
Omnibus - NCBI abundance study 2011
ArrayExpress at Any curated MIAME or MINSEQE October 28,
24838 708914
EBI compliant transcriptomics data 2011

private and published microarray and


Stanford Microarray October 23,
molecule abundance database (now 82542 ?
database 2011
defunct)

The Cancer
collection of expression data for different August 30,
Genome Atlas 21229 ?
cancers 2013
(TCGA)
Open access standard arrays, exons
GeneNetwork
arrays, and RNA-seq data for genetic ~100 ~10000 July, 2010
system
analysis (eQTL studies) with analysis suite

UNC modENCODE July 17,


Nimblegen customer 2.1 million array ~6 180
Microarray database 2009

data generated by microarray analysis November


UPSC-BASE ~100 ?
within Umeå Plant Science Centre (UPSC). 15, 2007
UPenn RAD MIAME compliant public and private Sept. 1,
~100 ~2500
database studies, associated with ArrayExpress 2007

provides the service for microarray data


UNC Microarray April 1,
storage, retrieval, analysis, and ~31 2093
database 2007
visualization

The database is a repository for DNA


microarray data generated by MUSC April 1,
MUSC database ~45 555
investigators as well as researchers in the 2007
global research community.
Cancer data, prepared for analysis on November
caArray at NCI 41 1741
caBIG 15, 2006

See also
Biological database
List of biological databases
DNA microarray
DNA microarray#Data warehousing
Microarray analysis techniques

External links
ArrayExpress: Quick Tour on EBI Train OnLine (http://www.ebi.ac.uk/training/online/course/a
rrayexpress-quick-tour)
Exploring functional genomics data with the ArrayExpress Archive on EBI Train OnLine (htt
p://www.ebi.ac.uk/training/online/course/arrayexpress-exploring-functional-genomics-data-a
r)
Investigating gene expression patterns with the Gene Expression Atlas on EBI Train OnLine
(http://www.ebi.ac.uk/training/online/course/arrayexpress-investigating-gene-expression-patt
ern-0)
ArrayExpress:Submitting data using MAGE-TAB on EBI Train OnLine (http://www.ebi.ac.uk/t
raining/online/course/arrayexpress-submitting-data-using-mage-tab)
ArrayExplorer (http://www.arrayexplorer.com) - A free tool to compare microarrays side by
side.

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