RESOURCESRESOURCES

Microarray Tool Kit

Tools and resources for the analysis, visualization and integration of gene expression data, including publically available microarray databases.

Arabidopsis Tillling Array Resource

http://signal.salk.edu/cgi-bin/atta

This site provides the transcription profile of the Arabidopsis genome (coding and non coding). Data from a range of tissue types and conditions are shown in a genome browser format along with the expression profiles for both DNA strands. Numerous other annotations such as the position of micro and small RNAs are also provided.

AREX: The Arabidopsis Gene Expression Database

http://www.arexdb.org/

Arex stores genome-wide (Affymetrix microarray) and gene-specific (in situ, GFP-reporter, etc.) Arabidopsis spatial gene expression data. Currently, Arex only stores data from the root.

From the abstract: We present microarray expression profiles of a high-resolution set of developmental time points within a single Arabidopsis root and a comprehensive map of nearly all root cell types. These cell type–specific transcriptional signatures often predict previously unknown cellular functions. A computational pipeline identified dominant expression patterns that demonstrate transcriptional similarity between disparate cell types.

Array Express

http://www.ebi.ac.uk/arrayexpress/#ae-main

The ArrayExpress Archive is a database of functional genomics experiments including gene expression where you can query and download data collected to MIAME and MINSEQE standards. Gene Expression Atlas contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments.

AtGenExpress

http://www.arabidopsis.org/portals/expression/microarray/ATGenExpress.jsp

A multinational coordinated effort to uncover the transcriptome of the multicellular model organism Arabidopsis thaliana. Contains data from a wide range of conditions and developmental stages.

CATMA, Complete Arabidopsis Transcriptome Microarray

http://www.catma.org/

A searchable database of Gene Specific Tags (GSTs) covering most Arabidopsis genes. There are currently 30,886 GST entries in the CATMA database.

From the abstract: The Complete Arabidopsis Transcript MicroArray (CATMA) initiative delivers gene-specific sequence tags (GSTs) for the Arabidopsis research community. These GST amplicons can easily be reamplified and shared, subsets can be picked at will to print dedicated arrays, and the GSTs can be cloned and used for other functional studies.This resource is also used both for the production of spotted microarrays and the large-scale cloning of hairpin RNA silencing vectors.

ColdArray DB

http://cold.stanford.edu/cgi-bin/data.cgi

A database that contains global expression profiles of Arabidopsis and tomato genes in response to cold temperatures. Currently researchers can search for expression profiles, cis-element information using a few input parameters, and download microarray experiment chip data.

eFP Browser

http://bbc.botany.utoronto.ca/efp/cgi-bin/efpWeb.cgi

The Arabidopsis electronic fluorescent protein browser (eFP) translates the developmental expression data generated by the AtGenExpress project in to a pictorial view. Users can either view where their gene is expressed or compare its pattern of expression to another locus of interest.

 

GEMMA

http://www.chibi.ubc.ca/Gemma/home.html;jsessionid=D1D347293DA71BC567F8C907DC500A13

Test for co-expression or differential expression of genes in different experiments. An existing database of over 3300 expression profiling studies which can be user-updated. 

From the abstract: Gemma is a database, analysis software system and web site for genomics data re-use and meta-analysis. Gemma currently contains analysed data from over 3300 expression profiling studies, yielding hundreds of millions of differential expression results and coexpression patterns (correlated expression) for retrieval and visualisation.

Genevestigator

https://www.genevestigator.com/gv/index.jsp

Genevestigator currently contains the world's largest compendium of high quality, manually curated expression data for plants (including Arabidopsis, tobacco, barley and rice) and microorganisms. The site is user friendly and contains a wide range of tools for analysing and querying a large database of microarray data from sources including NASC, AtGenExpress, FCGZ and the Gruissiem lab. The basic tool is free while more advanced tools are subscriber only. 

From the abstract: The databases currently comprise experiments from pathology, plant nutrition, abiotic stress, hormone treatment, genotype, and spatial or temporal analysis, but are expected to cover a broad variety of research areas as more experimental data become available.

GEO

http://www.ncbi.nlm.nih.gov/geo/

The Gene Expression Omnibus is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles.

Advice and instructions on using GEO to find and share Arabidopsis microarray data is provided on the GARNet blog

From the abstract: GEO stores over 20 000 microarray- and sequence-based functional genomics studies, and continues to handle the majority of direct high-throughput data submissions from the research community. Multiple mechanisms are provided to help users effectively search, browse, download and visualize the data at the level of individual genes or entire studies.

GLAMA

http://www.brc.dcs.gla.ac.uk/systems/glama/

The Functional Genomics Facility and the Bioinformatics Research Centre at the University of Glasgow have a set of microarray analysis tools available for researchers to use.

From the abstract: The new technique, which is based on calculating rank products (RP) from replicate experiments, is fast and simple. At the same time, it provides a straightforward and statistically stringent way to determine the significance level for each gene and allows for the flexible control of the false-detection rate and familywise error rate in the multiple testing situation of a microarray experiment.

MIAME

http://www.mged.org/Workgroups/MIAME/miame.html

A tool describing the Minimum Information about a microarray experiment that is needed for unambiguous interpretation and reproducibility. The public repositories ArrayExpress at the EBI (UK), GEO at NCBI (US) and CIBEX at DDBJ (Japan) are designed to accept, hold and distribute MIAME compliant microarray data.

From the abstract: Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it.

MIAME/Plant White Paper

http://www.arabidopsis.org/portals/expression/microarray/MIAME-plant_Dec2005.pdf

Standards for describing plant microarray experiments and samples.

NASC Arrays

http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl

A publicly available database of all microarray experiments carried out at the NASC facilities. NASC Arrays accepts data donations from the community. Their website includes a tips about methods, using their service, and Info for Newbies

Using GEO

http://blog.garnetcommunity.org.uk/tag/geo/

Advice on finding specific datasets on GEO, with Arabidopsis Affymetrix as an example, is provided in this post.

Advice on how to share your data on GEO is provided in this post