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

Alboukadel Kassambara, Thierry Rème, Michel Jourdan, Thierry Fest, Dirk Hose, Karin Tarte and Bernard Klein

PLOS Computational Biology, 2015, vol. 11, issue 1, 1-10

Abstract: DNA microarrays have considerably helped to improve the understanding of biological processes and diseases. Large amounts of publicly available microarray data are accumulating, 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 expression 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 differentiation using publicly available transcriptome data of naïve B cells, centroblasts, centrocytes, 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 analyses, 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.Author Summary: The use of DNA microarrays has emerged as a powerful tool for biomedical research to understand complex biological processes and diseases, generating large amounts of publicly available data. Most of these data remain unused by scientific community due to the lack of easy-to-use bioinformatics resources to analyze them. Here we present GenomicScape (www.genomicscape.com), a free online data-mining platform to identify quickly molecular changes during any biological process. As an example, we used GenomicScape to build a comprehensive and accessible molecular atlas of human B cell differentiation, which will be of great interest for immunologists to further understand normal and malignant B cell differentiation.

Date: 2015
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pcbi00:1004077

DOI: 10.1371/journal.pcbi.1004077

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