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
1 CHU Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, F-34000 France
2 INSERM, U847, Montpellier, F-34000 France
3 CHU Montpellier, Laboratoire d’Hématologie, Hôpital St-Eloi, F-34000 France
4 CNRS UMR 8147 and Department of Haematology, Hôpital Necker-Enfants-Malades Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-5 Descartes Paris, F-75015 Paris
5 Institute of Human Genetics, CNRS UPR-1142, Montpellier, F 34000 France
6 Université MONTPELLIER1, UFR de Médecine, Montpellier, F-34000 France
7 CHU Montpellier, Département de Médecine et Biologie de la Reproduction, Hôpital Arnaud de Villeneuve, Montpellier, F-34000
8 CHU Montpellier, Unité de Thérapie Cellulaire et Génique, Hôpital Saint-Eloi, Montpellier, F-34000 France


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© 2010 Le Carrour et al.

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.

* Address correspondence to this author at the Institute for Research in Biotherapy, Hôpital Saint-Eloi, 80 Avenue Augustin Fliche, 34295 Montpellier Cedex 5, France; Tel: +33 (0)4 67 33 01 91; Fax: 33 (0)4 67 33 79 05; E-mail: john.devos@inserm.fr


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/

Keywords: Pluripotent stem cells, Embryonic stem cells, Therapeutics, Cell reprogramming, Cell proliferation, Cell differentiation.