RESEARCH ARTICLE
Amazonia!: An Online Resource to Google and Visualize Public Human whole Genome Expression Data
Tanguy Le Carrour1, 2, Said Assou1, 2, Sylvie Tondeur1, 2, 3, Ludovic Lhermitte4, Ned Lamb5, Thierry Reme1, 2, Veronique Pantesco1, 2, Samir Hamamah1, 2, 6, 7, Bernard Klein1, 2, 6, John De Vos*, 1, 2, 6, 8
Article Information
Identifiers and Pagination:
Year: 2010Volume: 4
First Page: 5
Last Page: 10
Publisher ID: TOBIOIJ-4-5
DOI: 10.2174/1875036201004010005
Article History:
Received Date: 11/11/2009Revision Received Date: 23/12/2009
Acceptance Date: 23/12/2009
Electronic publication date: 27/01/2010
Collection year: 2010
open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: https://creativecommons.org/licenses/by/4.0/legalcode. This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
Available transcriptome data accumulate in public repositories, individual web pages or as various supplemental data, but these published data cannot be routinely accessed. We have developed the web based tool Amazonia! to overcome this hurdle and provide the possibility to query and to visualize the expression of a given gene in representative and selected human transcriptome datasets. This expression atlas provides expression bar plots for single genes, across samples selected from a wide range of normal tissues and malignancies, including pluripotent stem cells. When produced by the same platform type, datasets were renormalized and combined in order to generate series of several hundreds samples. Samples types are colored and ordered, and grouped in thematic pages for ease of navigation. We also integrated gene lists provided by original publications describing these microarray data, allowing the scientific community to challenge the expression of genes in datasets other than those for which they were initially published. To illustrate the powerfulness of this simple tool, we show how Amazonia! reveals the specific expression of the tight junction protein Claudin 6 in human embryonic stem cells and human induced stem cells (iPS), or the tissue specific expression of some chemokines and their receptors such as CCL16 in liver and CX3CR1 in central nervous system samples. Thus, Amazonia! advantageously complements large public repositories by providing a simple way to query a compilation of selected human transcriptome data.
The tool is freely available at http://www.amazonia.transcriptome.eu/
