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New and Updated Online Tutorials for ArrayExpress, Allen Brain Atlas and CleanEx from OpenHelix

Comprehensive tutorials on the publicly available ArrayExpress, Allen Brain Atlas and CleanEx databases enable researchers to quickly and effectively use these invaluable resources.

Seattle, WA (PRWEB) August 13, 2009 -- OpenHelix today announced the availability of new tutorial suites on ArrayExpress, Allen Mouse Brain Atlas and CleanEx. ArrayExpress is one of the largest international public repositories for storage and sharing of gene expression and other microarray data. Allen Mouse Brain Atlas, from the Allen Brain Institute is a database of spatially mapped large-scale gene expression data from a genome wide survey of expression patterns in the C57BL/6J adult mouse brain. CleanEx provides an online database of genome-wide gene expression data. These three new tutorials in conjunction with additional OpenHelix tutorials on DAVID, VISTA, GEO, DBTSS, NCBI Entrez and many others, give the researcher an excellent set of training resources to assist in their gene expression research.

The tutorial suites, available for single purchase or through a low- priced yearly subscription to all OpenHelix tutorials, contain an online, narrated, multi-media tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. These tutorials will teach users:

Array Express

  • to query the archive of ArrayExpress for records of experiments, arrays, and protocols, and to export data
  • to query for expression profiles of genes, and identify groups of genes with similar expression profiles
  • to find conditions under which a gene is differentially expressed, and to find genes differentially expressed under certain conditions

Allen Brain Atlas
  • to access the Allen Reference Atlas, atlas legend, and structure ontology
  • to perform effective gene expression searches of the Allen Mouse Brain Atlas
  • to locate gene expression image datasets from the search results using the List View and Thumbnail Views
  • how to use the Single and Multiple Image Viewers
  • how to download and use the Brain Explorer application

  • to find information on transcript abundance and expression targets by gene names
  • to extract numerical expression data from CleanEx
  • to search for datasets or subsets representing biological conditions of interest, using MeSH terms
  • to identify over- or under-expressed genes in a dataset, and examine the expression pattern of these genes in other datasets
  • to identify genes whose expression levels correlate with a biological condition across multiple datasets

With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others.
To find out more about these and over 70 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About OpenHelix:

OpenHelix, LLC, ( provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web-based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.


Scott Lathe
(888) 861-5051


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