title: 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 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.
authors: U1040, INSERM, Montpellier, France; Department of Biological Hematology, CHU Montpellier, Montpellier, France.
authors: Alboukadel
authors: A
authors: Kassambara
authors: U1040, INSERM, Montpellier, France; Department of Biological Hematology, CHU Montpellier, Montpellier, France.
authors: Thierry
authors: T
authors: Rème
authors: U1040, INSERM, Montpellier, France.
authors: Michel
authors: M
authors: Jourdan
authors: U917, INSERM, Rennes, France.
authors: Thierry
authors: T
authors: Fest
authors: Medizinische Klinik V, Universitätsklinikum Heidelberg and Nationales Centrum für Tumorerkrankungen, Heidelberg, Germany.
authors: Dirk
authors: D
authors: Hose
authors: U917, INSERM, Rennes, France.
authors: Karin
authors: K
authors: Tarte
authors: U1040, INSERM, Montpellier, France; Department of Biological Hematology, CHU Montpellier, Montpellier, France; UFR Médecine, Université MONTPELLIER 1, Montpellier, France.
authors: Bernard
authors: B
authors: Klein
mesh_terms: D001402:B-Lymphocytes / Q000166:cytology*; D002454:Cell Differentiation / Q000502:physiology*; D016000:Cluster Analysis; D057225:Data Mining; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods*; D006801:Humans; D020407:Internet; D010950:Plasma Cells / Q000166:cytology*; D025341:Principal Component Analysis; D012984:Software
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