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GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells

Abstract : DNA microarrays have considerably helped to improve the understanding of biological pro-cesses and diseases. Large amounts of publicly available microarray data are accumulat-ing, but are poorly exploited due to a lack of easy-to-use bioinformatics resources. The aim of this study is to build a free and convenient data-mining web site (www.genomicscape. com). GenomicScape allows mining dataset from various microarray platforms, identifying genes differentially expressed between populations, clustering populations, visualizing ex-pression profiles of large sets of genes, and exporting results and figures. We show how easily GenomicScape makes it possible to construct a molecular atlas of the B cell differen-tiation using publicly available transcriptome data of naïve B cells, centroblasts, centro-cytes, memory B cells, preplasmablasts, plasmablasts, early plasma cells and bone marrow plasma cells. Genes overexpressed in each population and the pathways encoded by these genes are provided as well as how the populations cluster together. All the analy-ses, tables and figures can be easily done and exported using GenomicScape and this B cell to plasma cell atlas is freely available online. Beyond this B cell to plasma cell atlas, the molecular characteristics of any biological process can be easily and freely investigated by uploading the corresponding transcriptome files into GenomicScape.
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https://hal-univ-rennes1.archives-ouvertes.fr/hal-01112225
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Submitted on : Monday, February 2, 2015 - 2:35:39 PM
Last modification on : Wednesday, October 14, 2020 - 1:23:02 PM
Long-term archiving on: : Wednesday, May 27, 2015 - 3:42:22 PM

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Alboukadel Kassambara, Thierry Rème, Michel Jourdan, Thierry Fest, Dirk Hose, et al.. GenomicScape: An Easy-to-Use Web Tool for Gene Expression Data Analysis. Application to Investigate the Molecular Events in the Differentiation of B Cells into Plasma Cells. PLoS Computational Biology, Public Library of Science, 2015, 11 (1), pp.e1004077. ⟨10.1371/journal.pcbi.1004077⟩. ⟨hal-01112225⟩

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